NAD phosphorylation and dephosphorylation

MetaCyc:NADPHOS-DEPHOS-PWY

The native NAD phosphorylation and dephosphorylation pathway contains three core transformations: ATP-dependent NAD phosphorylation, NADP hydrolysis, and proton-coupled transhydrogenation. The E. coli evidence supports individual activities and condition-dependent nucleotide balancing, but does not identify the physiological cytosolic NADP phosphatase or establish a complete cycle in every strain. The broader native taxonomic range is curated pathway scope, not a measurement of flux in every listed organism. Soluble SthA is included as an opposing supporting redox activity, outside the three native member reactions. The exact directional reactions are RHEA:18630, NAD(1−)+ATP(4−)→NADP(3−)+ADP(3−)+H+; RHEA:28051, NADP(3−)+water→NAD(1−)+hydrogenphosphate(2−); and RHEA:47994, NADH(2−)+NADP(3−)+H+(outside)→NAD(1−)+NADPH(4−)+H+(inside). Each side has coefficient one. The two proton appearances are distinct transport sides and are not canceled. RHEA:11693 describes the supporting soluble NAD(1−)+NADPH(4−)→NADH(2−)+NADP(3−) reaction without proton transport. Compartments remain explicit in the source participants and edge descriptions; one shared proton chemical identity does not erase the transport. Frozen PathBank SMP0002093/PW002081 corroborates the three-event boundary: two BiochemicalReaction objects plus one TransportWithBiochemicalReaction. Its class-specific count of two does not mean that the transport event is absent. Its NAD, NADH, NADP, NADPH, ATP, ADP and phosphate references use CHEBI:15846,16908,18009,16474,15422,16761 and18367, respectively, rather than all of the exact Rhea charge forms. Those forms are not asserted to be exact chemical matches. The frozen diagram also assigns both transport protons to the same Inner_Membrane entity; it supplies structural context, not inside/outside topology or physical membrane localization of the nucleotide pools. NadK is a homohexamer in the native assembly and the 2001 purification, approximately180 kDa with approximately30-kDa subunits. The native assembly object CPLX0-682 has no direct name, so its display remains unnamed while its six-chain NadK interpretation is stated here. Endogenous MG1655 protein was purified3400-fold after growth at37°C for18 h. Its measured N terminus MDNHFKCIGI differs at residue2 from the deduced/current reference MNNHFKCIGI. The separately expressed pSK67 yfjB construct used pET14b NcoI/BamHI in BL21(DE3)pLysS, with empty SK45 as control; the vector name alone does not establish a retained His tag. The reference NadK is cytoplasmic by reviewed rule-based annotation, with an annotated proton-accepting residue73; the historical preparations are not assigned that exact sequence merely by accession. The 2001 purified-NadK assay used5 mM NAD and ATP,5 mM MgCl2,100 mM Tris at pH7.0 and37°C. At5 mM donor, reported relative activities were ATP100%, UTP109%, CTP60%, GTP56%, dATP42% and TTP40%. These alternate in-vitro donors do not redefine the native ATP core. Polyphosphate at1 mg/mL and the tested pyrophosphate, tripolyphosphate, trimetaphosphate, hexametaphosphate, metaphosphate, ADP, AMP, phosphoenolpyruvate, phosphocreatine, glucose6-phosphate and p-nitrophenylphosphate did not support the measured phosphorylation. NADH, ADP-ribose, adenosine, AMP, ADP and ATP were not phosphorylated as acceptors in experiments described as data not shown. Activity peaked near pH7.5 and60°C;65°C for10 min removed about half the activity. Replacing the divalent metal at1 mM gave relative NadK activities Mg100%, Mn242%, Zn104%, Ca85% and Co73%. FeCl2, CuCl2, NaCl, KCl, LiCl and no-metal conditions gave no detected activity in that replacement experiment. Failure to substitute for Mg is not inhibition of an Mg-containing assay. The supported metals are alternatives, not a claim that all occupy the hexamer simultaneously or that the fastest in-vitro metal is physiologically preferred. The 1987 NadK preparation came from an unspecified E. coli K12 substrain grown in forced-aerated glycerol minimal medium at37°C and harvested in late log phase. It was enriched93-fold and was explicitly not homogeneous. The general assay used 10 mM NAD and 10 mM ATP, 14 mM MgCl2 and 100 mM MOPS at pH 7.2. Table 2 instead used 4.0 mM NAD, found that roughly tenfold more NADH than NADPH was needed for similar inhibition, and reported additive inhibition when both were present. Separate saturation experiments varied NAD, using NADPH at 5–30 µM or NADH at 50–200 µM. NAD saturation became sigmoidal, with reported Hill coefficients1.8–2.1 for NADPH and1.7–2.0 for NADH; increasing NAD could overcome inhibition. These kinetic observations and native allosteric annotations do not locate a binding site experimentally. The abstract assigns Km1.9 mM to NAD and2.1 mM to ATP, whereas the Results reverse those assignments; both are retained as an internal discrepancy. In the 2001 preparation, NADPH at5 and10 µM left58% and24% activity, while NADH left68% and39%. NADP at50 and100 µM left83% and79%, contrasting with the absence of a significant NADP effect in the 1987 conditions. Quinolinate, nicotinate, nicotinamide, nicotinamide mononucleotide, ADP and AMP likewise had no significant effect in the earlier experiment. Varying adenylate energy charge from0 to1 at4 mM total adenylates, with or without15 µM NADPH, did not change the 1987 rate. Those negative findings are condition-limited and do not imply that adenylate composition never influences nucleotide metabolism. The 2001 NadK thiol-reagent experiment used a glucose6-phosphate dehydrogenase reporter instead of the inhibitor-sensitive isocitrate dehydrogenase reporter. DTT,2-mercaptoethanol and glutathione at1 mM left100% activity. PCMB at1,0.25 and0.1 mM gave no detected activity,33% and51%; HgCl2 gave no detected activity,35% and54%. HgCl2 remains the salt, not a free-mercury node. The unspecified PCMB salt/charge is retained as reagent prose rather than forced onto an acid or anion identity. Table3 reports its own kcat values55/125 and efficiencies22/38; these are not silently recalculated from another table. Failed recovery of a yfjB disruption, described as data not shown, suggested essentiality under those conditions rather than proving universal essentiality. The 2005 primary abstract and issuing NadK variant annotations distinguish R175G/H/Q/T, which gain NADH-kinase activity, from R175E/I/K, which do not. R175G also lowers the NAD-kinase Vmax. These variants are not assigned to the wild-type endpoint and do not contradict the negative wild-type acceptor assay. The full 2005 body was unavailable. The native physiological NADP-phosphatase object has no assigned gene. Purified alkaline phosphatase converted historical TPN to DPN in the 1962 source, supporting in-vitro NADP hydrolysis. That paper used GL, BAP, PV and HH preparations with AMP-based specific activities1230,1130,1130 and1060 units/mg, but the TPN sentence identifies neither a particular fraction nor an E. coli strain. Its standard assayA contained0.05 M Tris pH8.2,0.01 M substrate and0.2–1 enzyme units in0.5 mL for20 min at37°C; assayB used p-nitrophenylphosphate at4×10−4 M. No exact reference sequence, processing isozyme or particular fraction is retrospectively assigned to the TPN observation. Reviewed PhoA is periplasmic, with a1–21 signal peptide and a mature reference chain beginning at22. Its Ser124 annotation describes the phosphoserine catalytic intermediate. The reference binds two Zn ions and one Mg ion per subunit; these are per-chain capacities, not three coefficient-one ions assigned indiscriminately to a whole dimer. Isozymes1 and3 have identical-chain dimers, whereas isozyme2 combines the differently processed chains. DsbA-assisted folding and Iap-related N-terminal processing are protein-maturation context, not evidence for NADP-specific regulation. The native report of additional phosphite oxidation is a separate PhoA function, not another NADP-core reaction. Periplasmic localization and the native enzyme record’s physiological-relevance flag do not establish a cytosolic recycling loop. The 1962 PhoA inhibitor/activation observations largely concern p-nitrophenylphosphate or AMP, not NADP. They include strong cadmium inhibition, urea effects that depend on exposure time and can reverse, and substrate/salt-dependent stimulation; the text reports activating fluoride and p-hydroxymercuribenzoate conditions and more modest mercury/cobalt effects. Competitive phosphate inhibition is discussed with prior-work attribution. Mg plus phosphate can protect against heat inactivation, while concentrated NaCl can worsen it; KCl can block recovery and fluoride, urea or CuSO4 can slow recovery in their stated experiments. The flattened primary-table rendering does not justify invented precise row/column values, and none of these broad-substrate or renaturation results is relabeled a direct inhibition measurement of NADP turnover. The 2007 CysQ preparation was the GFP-free ASKA AG1 pCA24N construct, carrying N-terminal His6 plus TDPALRA and C-terminal GLCGR extensions. At37°C, pH8.0 and10 mM MgCl2 it hydrolyzed NADP and NADPH. Reported Km and kcat were2.70±0.53 mM and0.70±0.09 s−1 for NADP, and2.13±0.25 mM and1.45±0.18 s−1 for NADPH. The additional NADPH substrate activity is retained as assay context, not an extra member of the three-event core. PAP preference and the different optima led the authors to conclude that CysQ probably is not the physiological E. coli NADP phosphatase. CysQ NADP(H)ase activity was undetectable at pH6.4 or0.2 mM Mg, conditions more favorable to its PAPase. Matched Fbp and SuhB extracts were negative controls;15 mM NaCl,7.5 mM imidazole and2.5% glycerol carried with the preparation did not explain the activity. LiCl IC50 values were70 mM for NADP,60 mM for NADPH,10 mM for FBP,0.05 mM for3-PAP and0.15 mM for2-PAP; table dashes mean not determined. Reviewed CysQ calcium/lithium inhibition from the separate 2006 nucleotidase study is general protein context, not a calcium experiment on the 2007 NADP assay. Its annotated peripheral inner-membrane location is on the cytoplasmic side and still does not resolve the physiological catalyst. The 2007 archaeal comparisons used MJ0109, AF2372 and MJ0917 constructs in separately specified BL21/OrigamiB expression contexts and assays at85°C with20 mM Mg, pH8.5. Their activities are not assigned to E. coli CysQ or to one physiological E. coli loop. A later paper’s estimate of approximately140 NADP molecules dephosphorylated per cell per second is a citation to older work, not a firsthand reconstruction of that experiment. The 1971/1973 primary bodies and abstracts were unavailable; their bibliographic records and native/later-paper framing remain explicitly secondary evidence for the historical turnover claim. PntAB is a dimer of heterodimers: two PntA and two PntB chains in the native complex. The UniProt heterodimer description denotes the protomer and does not conflict with the α2β2 assembly. Its cytoplasmic nucleotide-binding domains dI and dIII handle NAD(H) and NADP(H), while membrane domain dII couples them to proton movement; FAD is not assigned as a Pnt cofactor. Native historical annotation gives AB (Re–Si) specificity, transferring the pro-R hydrogen of NADH and pro-S hydrogen of NADPH; this is not a new stereochemical measurement in the 2021 experiment. The 2021 pSA2-derived pET16b construct was expressed in THO C43(DE3) Δcyo ΔpntAB with an alpha N-terminal His6 tag and thrombin site. Tag cleavage was not reported. DDM-purified protein and proteoliposomes represent distinct preparations. The 2021 natural forward NADH/NADP and reverse NADPH/NAD assays used their stated regenerating systems; APAD-dependent reverse and cyclic assays were separate. The cyclic reaction does not carry net proton transport. Reported apparent Km values were NADPH4.1±1.2 µM, NAD108±12 µM, NADP37±7 µM and NADH6.8±1 µM. The source gives fixed NADH as50 µM in Methods but500 µM in Results; those descriptions are not silently reconciled. Reconstitution incorporated65±10% protein, with approximately75±5% of reverse-active and85±5% of cyclic-active sites facing outward. These are proteoliposome orientation estimates, not an inversion of cellular topology. Reverse Pnt hydride transfer generated a proton gradient and supported a co-reconstituted ATP synthase. The βH91A variant, no-enzyme controls and ionophores tested the coupling; ATP synthesis belongs to the separate ATP synthase, not the Pnt stoichiometry. An ATPase-generated proton motive force stimulated NADPH formation7±1.8-fold without ionophore,6.4±0.8-fold with valinomycin, and1.6±0.3-fold with CCCP plus valinomycin. The proposed gated-channel and dIII-flip mechanisms are mechanistic interpretations. Thermus thermophilus structural models and prior domain experiments do not become an experimental E. coli full-complex structure. Older Pnt inhibitor papers were available as primary abstracts and native annotations. DCCD inhibits transhydrogenation and proton pumping; NADH protects, while NADP and, less strongly, NADPH accelerate inhibition. In the 1993 αD232/E238/E240 mutant series, the proteins retained40–90% activity and proton pumping, while triple substitutions reduced DCCD sensitivity. Those historical residues/preparations are distinct from the 2021 βH91A construct. NBD chloride modifies βC147/260 and other residues; NADPH protects some domain modification, but an NBD–NADPH reaction product is itself strongly inhibitory. The adduct has no invented exact chemical identity here. The 1999 Pnt topology abstract used cysteine-free, His-tagged single-cysteine variants in intact cells and inside-out membranes, supporting four alpha and nine beta membrane spans in that experimental model. Native comments also preserve older nucleotide-affinity, cysteine-free and βD213 contexts. These are source-specific topology and kinetic studies, not measurements on the 2021 preparation. Reference-chain residue numbering, domain models, tags and assay directions remain distinct. Soluble SthA, also called UdhA, is represented as an octamer with reference P27306. The 1999 cloning abstract corrected an N-terminal genome-sequencing error; its older7–8-subunit interpretation is retained alongside the exact native octamer and the later approximately440-kDa SEC/DLS estimate. The 2022 K12 sthA construct carried a C-terminal His10 tag in pBXC3H and was expressed in MC1061; FAD was added during lysis before affinity and SEC purification. Reviewed capacity is one FAD per subunit, whereas a native historical comment reports measured occupancy0.76 mol FAD/subunit. Partial FAD loss during SEC is preparation-dependent. Native B-stereospecificity is explicitly not experimentally determined. The 2022 kinetic assay followed NADH/thioNADP transhydrogenation, opposite to the supporting physiological NADPH-to-NAD reaction. ThioNADP is a surrogate, not NADP. At5 mM, AMP, ADP and ATP raised wild-type activity to160.7±2.9%,171.1±7.2% and148.2±8.9%. Corresponding C45A values were454.9%,991.8% and363.1%; T50C values were222.9%,319.2% and177.4%. Each series uses its own no-adenylate baseline:8.66±0.83,0.55±0.10 and0.92±0.18 µmol/min/mg for wild type, C45A and T50C. Large mutant percentages therefore do not imply higher absolute mutant activity or restore the wild-type mechanism. Sodium and potassium phosphate inhibited the 2022 SthA surrogate assay, approaching residual activities of approximately20–25% and15% around50 mM. NaCl/KCl controls showed no significant change through50 mM, but500 mM left approximately70% and40%; high ionic strength is not universally inert. The hydrogenphosphate reference node denotes phosphate-buffer chemistry, not isolation of one protonation species. NADH above7 mM gave substrate inhibition with KI12.1±2.0 mM at0.5 mM thioNADP; thioNADP itself had KI0.59±0.26 mM. Neither observation establishes inhibition by natural NADP under all conditions. SthA can also oxidize NADH or NADPH with oxygen in uncoupled assays, releasing predominantly hydrogen peroxide with some superoxide. No-enzyme blanks and anaerobic persistence of reduced flavin constrain that interpretation. The wild-type coupled assay partitioned approximately98% to thioNADPH and2% to ROS; C45A gave62.3% hydride-transfer and37.1% peroxide-associated partitioning, while T50C gave89.2% and10.2%, at much lower total transfer rates. Reported flavin-reduction k_red/Kd were303±50 s−1/88±27 µM for wild type,710±160/300±100 for C45A and2200±400/227±61 for T50C. These mutant and side-activity observations do not add an oxygen-consuming core reaction or establish a universal cellular ROS flux. The 2022 paper distinguishes the reference P27306 sequence from AlphaFold model AF-B7M718-F1 and modeling with Thermus thermophilus lipoamide dehydrogenase2EQ7; these are not an experimental structure of the exact reference chain. A12-nucleotide sthA/oxyR overlap motivated a redox-stress hypothesis but did not demonstrate an OxyR→sthA regulatory edge. The 2011 purified fused-EcSTH primary abstract describes NADPH/thio-NAD activity, Km68.29 and133.2 µM, optimum35°C and pH7.5, stimulation by adenylates at2 mM, and inhibition by Mn, Co, Zn, Ni and Cu. After30 min preincubation, strong inhibition persisted only for Zn, Ni and Cu. Full Methods and the exact fusion sequence were unavailable. Its description of excess-NADPH product inhibition is preserved as the source’s terminology even though NADPH is the named assay substrate; it is not converted into a different reaction direction. These abstract-level results do not replace the 2022 salt controls or wild-type His10 preparation. In the 2004 MG1655 deletion/13C study (PMID:14660605), aerobic M9 cultures at37°C with5 g/L carbon source supported different physiological roles: PntAB supplied an estimated35–45% of biosynthetic NADPH during glucose growth, while loss of pntAB slowed growth and increased oxidative pentose-phosphate compensation. Soluble UdhA was important on acetate and in a pgi-deficient state with excess NADPH, rather than being required for ordinary glucose growth in that study. Some complementation results were described as data not shown. Crude-extract NADPH/APAD reverse assays measured enzyme capacity, not the same quantity as in-vivo redox flux. A 2004 redox-linked transcriptional interpretation (PMID:14660605) was later tested more directly: the 2016 study (PMID:27488847) found no correlation of transhydrogenase promoter activities with NADPH pools or formation/consumption fluxes across the tested perturbations. Paraquat at10 µM induced the zwf positive control without inducing pntAB or sthA. This narrows the earlier model under those conditions; it does not assert that every redox perturbation is transcriptionally inert. The 2016 regulatory screen compared BW25113 with62 Keio transcription-factor deletions using low-copy whole-intergenic gfpmut2 reporters containing50–100 bp flanks. M9 cultures contained5 g/L glucose, glycerol or succinate at37°C; mid-exponential OD-normalized activity was taken over OD6000.7–1.5. All screen rows retain growth rates and deviations; most had two biological replicates and selected validations three. These are conditional expression responses. Below-threshold differences are not proof of absence, and a deletion response alone does not demonstrate direct promoter binding. IHF-alpha deletion reduced pntAB reporter activity to approximately0.15,0.16 and0.12 of wild type on succinate, glycerol and glucose, respectively. The IHF reference is an alpha/beta heterodimer; native component slots have no explicit coefficients, so the source descriptions are retained without inventing new component counts. Lrp deletion gave pntAB ratios0.43,0.42 and0.22 and sthA ratios1.43,1.68 and1.83 in the same carbon-source order; the main interpretation emphasized activation/repression on glycerol and glucose. ArgP activation of pntAB was identified on glucose and Fur activation on succinate. The proteins’ exact promoter-bound assemblies or metal states were not measured in this reporter study. The aerobic 2016 ArcA-deletion experiment increased sthA expression on glucose, but did not detect ArcA activation of pntAB. This is distinct from the 2014 anaerobic MG1655 study: ArcA-8myc ChIP and ΔarcA expression comparisons in M9 with0.2% glucose and0.1% ammonium chloride, with or without20 mmol KNO3 at37°C, supported pntAB activation and sthA repression. Native PHOSPHO-ARCA remains the cited active state, mapped to reference ArcA with phosphoaspartate54. The original supplementary promoter-region peaks and occupancies are retained in the evidence ledger; modern coordinates are not substituted for that source genome version. With a20-amino-acid mixture, H-NS and CRP repressed the pntAB reporter; basal-medium results were different, including CRP-deletion glucose ratios0.53 for pntAB and0.57 for sthA and failure of that mutant to grow on glycerol or succinate. Supplementary mixture-condition pntAB activities were WT274.91±5.93, H-NS deletion630.91±16.85, CRP deletion499.85±29.74, IHF deletion139.95 and Lrp deletion319.20. TyrR deletion lowered sthA activity from WT801.20±167.35 to332.83±14.09 in this supplementary screen. This supports conditional expression effects, not a measured direct interaction or a universal sign. At5 mM single amino acid, leucine lowered pntAB and increased sthA reporter activity; lysine and histidine lowered pntAB, and methionine increased sthA. Valine prevented growth in that experiment and is not assigned an inhibitory promoter edge. Exact reference amino-acid charge forms identify the molecules without claiming that the medium contained an isolated ionic species. Exogenous cAMP reduced normalized pntAB activity by roughly50%, with only a marginal sthA decrease, after normalization to two constitutive reporters and verification of increased CRP activity. Native cAMP-bound CRP and the CRP dimer are represented, but the native component slots provide no ligand coefficient; direct pntA binding and occupancy were not measured. The 2019 Lrp source used MG1655 ATCC47076 versus lrp::kan in MOPS0.2% glycerol,37°C,200 rpm, with MIN log OD6000.15–0.25 and transition OD6001.8–2.2. Native located assertions assign Lrp activation of pntA in log phase and phoA in transition, and repression of sthA in log phase. The full primary Methods were inspected, but the exact per-gene supplementary data were unavailable, so these target-level statements remain native curated assertions. The His-tagged Lrp used to generate antibody is not a tag on the cellular ChIP endpoint. The 2017 Nac/CsiR study induced FLAG-tagged regulators from pT7-FLAG-4 in MG1655 in LB,1 mM IPTG for2 h from OD6000.2, with paired ChIP-seq and RNA-seq. Nac’s bound pntA row has peak1675942, coverage45, distance−15 and published normalized FC0.372191; this is not the raw4.3/13.24 ratio. Its cysQ row has peak4434633, coverage22, distance−145 and FC2.176844. Target assignment used the study’s proximity/operon framework, not promoter-specific site mutagenesis. Separate30°C nitrogen-depletion validation does not define these two rows or establish CysQ as the physiological NADP phosphatase. All16 selected-gene workbook rows are retained, including duplicate pntB operon annotations. CsiR, now called GlaR in the issuing reference, gave RNA-seq fold changes cysQ1.407187, nadK0.754291, phoA0.756034, pntA2.793539, pntB0.440537 and sthA0.587882; neither pntA nor pntB appeared in its bound-target sheet. Their opposite expression signs are preserved as potentially indirect responses. Corresponding Nac values were cysQ2.176844, nadK0.683302, phoA0.878483, pntA0.372191, pntB0.645038 and sthA0.879588. The ratios outside the bound Nac joins are quantitative context without invented statistical significance or blanket promoter-binding edges. Phosphorylated PhoB activates phoA through the exact native regulator→promoter PM00071→transcription-unit TU00052→phoA join. Its reference is P0AFJ5/phoB/b0399,229 residues, with phosphoaspartate53 and phosphorylation-dependent dimer orientation retained in the endpoint. P0A9I3 is GcvR and is explicitly rejected as PhoB. The 2013 acidic/aerobic versus microaerobic findings are available only through the primary abstract and native context, not full-body access. The 2019 phosphate-starvation reporter work (PMID:30765722) used MG1655 promoter fragments, BCD2/msfgfp and pSEVA234/237 plasmids in DH10B resting cells at30°C over0–50 mM phosphate; synthetic Pliar constructs and modeled phosphorylation/feedback rates are separate from measured native-promoter outputs. Spot42 represses sthA in MG1655-derived strains. The 2011 Northern experiment used NM525 Δspf GS0433 with IPTG-induced pSpot42; the translational-fusion experiment used PM1205 Δspf GS0434 with pBAD sthA-lacZ from its TSS through9–15 codons,0.2% arabinose and ±1 mM IPTG for1 h. The table reports a−4.2±0.5 expression change. RegionIII mutation and compensatory target mutation support direct RNA pairing. The 2012 follow-up (PMID:22388518) discusses multiple pairing regions, including I and III, without establishing simultaneous binding stoichiometry. Its nanC structural probing and Hfq-deletion experiments are not transferred to sthA; the sthA Hfq context in the earlier table retains that earlier source’s evidence level. Regulator reference annotations are retained separately from the pathway experiments. Lrp and ArgP have homodimer annotations; H-NS can form dimers and higher oligomers; TyrR changes between dimeric and tyrosine/ATP-associated higher assemblies. TyrR ATP binding enhances tyrosine affinity, but no particular TyrR assembly was measured at sthA. H-NS Lys121 hydroxyisobutyrylation, Fur His118 UMPylation, ArgP proteolysis, and GlaR glutarate relief of repression at glaH are known protein contexts, not demonstrated intermediates of the transhydrogenase reporter responses. Those unrelated target-specific mechanisms are not recursively imported as new pathway regulatory edges. The bounded iModulonDB check queried the six exact pathway loci and inspected ten selected module-member tables. None contained an exact target-locus match in that selection; alias/product substring matches were excluded. This is computational context and a bounded negative result, not global absence from iModulonDB or causal regulatory evidence. The Pseudomonas PathBank kinase/transhydrogenase definition with an unresolved protein and the archaeal phosphatases remain separate cross-source candidates, not organism-equivalent substitutes for the E. coli evidence.

Pathway type

cofactor metabolism

Organism scope

Escherichia coli NCBITaxon:562

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Pathway network

115 nodes · 102 asserted directed edges

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Escherichia coli `NCBITaxon:562`	taxon
NAD(1-) `CHEBI:57540`	small molecule
ATP(4-) `CHEBI:30616`	small molecule
ADP(3-) `CHEBI:456216`	small molecule
NADP(3-) `CHEBI:58349`	small molecule
hydron `CHEBI:15378`	small molecule
water `CHEBI:15377`	small molecule
hydrogenphosphate `CHEBI:43474`	small molecule
NADH(2-) `CHEBI:57945`	small molecule
NADPH(4-) `CHEBI:57783`	small molecule
adenosine 5'-monophosphate(2-) `CHEBI:456215`	small molecule
mercury dichloride `CHEBI:31823`	small molecule
lithium chloride `CHEBI:48607`	small molecule
1,3-dicyclohexylcarbodiimide `CHEBI:53090`	small molecule
4-chloro-7-nitrobenzofurazan `CHEBI:78878`	small molecule
L-leucine zwitterion `CHEBI:57427`	small molecule
L-lysinium(1+) `CHEBI:32551`	small molecule
L-histidine zwitterion `CHEBI:57595`	small molecule
L-methionine zwitterion `CHEBI:57844`	small molecule
3',5'-cyclic AMP(1-) `CHEBI:58165`	small molecule
magnesium(2+) `CHEBI:18420`	cofactor
manganese(2+) `CHEBI:29035`	cofactor
zinc(2+) `CHEBI:29105`	cofactor
calcium(2+) `CHEBI:29108`	cofactor
cobalt(2+) `CHEBI:48828`	cofactor
FAD(3-) `CHEBI:57692`	cofactor
iron(2+) `CHEBI:29033`	small molecule
copper(2+) `CHEBI:29036`	small molecule
NAD kinase `UniProtKB:P0A7B3`	protein
Alkaline phosphatase `UniProtKB:P00634`	protein
NAD(P) transhydrogenase subunit alpha `UniProtKB:P07001`	protein
NAD(P) transhydrogenase subunit beta `UniProtKB:P0AB67`	protein
Soluble pyridine nucleotide transhydrogenase `UniProtKB:P27306`	protein
3'(2'),5'-bisphosphate nucleotidase CysQ `UniProtKB:P22255`	protein
Aerobic respiration control protein ArcA `UniProtKB:P0A9Q1`	protein
Phosphate regulon transcriptional regulatory protein PhoB `UniProtKB:P0AFJ5`	protein
Leucine-responsive regulatory protein `UniProtKB:P0ACJ0`	protein
Nitrogen assimilation regulatory protein nac `UniProtKB:Q47005`	protein
DNA-binding transcriptional dual regulator CRP `UniProtKB:P0ACJ8`	protein
Integration host factor subunit alpha `UniProtKB:P0A6X7`	protein
Integration host factor subunit beta `UniProtKB:P0A6Y1`	protein
DNA-binding protein H-NS `UniProtKB:P0ACF8`	protein
HTH-type transcriptional regulator ArgP `UniProtKB:P0A8S1`	protein
Ferric uptake regulation protein `UniProtKB:P0A9A9`	protein
HTH-type transcriptional regulatory protein TyrR `UniProtKB:P07604`	protein
HTH-type transcriptional repressor GlaR `UniProtKB:P37338`	protein
unnamed protein complex CPLX0-682 `EcoCyc:CPLX0-682`	complex
alkaline phosphatase `EcoCyc:ALKAPHOSPHA-CPLX`	complex
PntAB `EcoCyc:PYRNUTRANSHYDROGEN-CPLX`	complex
soluble pyridine nucleotide transhydrogenase `EcoCyc:UDHA-CPLX`	complex
DNA-binding transcriptional dual regulator IHF `EcoCyc:PC00027`	complex
CRP-cyclic-AMP DNA-binding transcriptional dual regulator `EcoCyc:CPLX0-226`	complex
small regulatory RNA Spot 42 `EcoCyc:SPF-RNA`	rna
phoA `Entrez:945041`	gene
pntA `Entrez:946628`	gene
pntB `Entrez:946144`	gene
sthA `Entrez:948461`	gene
cysQ `Entrez:948728`	gene
cytosol `GO:0005829`	cellular component
plasma membrane `GO:0005886`	cellular component
periplasmic space `GO:0042597`	cellular component
nickel(2+) `CHEBI:49786`	small molecule
DNA-binding transcriptional dual regulator CRP `EcoCyc:PC00004`	complex
NAD(+) + ATP => ADP + NADP(+) + H(+) `RHEA:18630`	molecular activity	left to right
NADP(+) + H2O => phosphate + NAD(+) `RHEA:28051`	molecular activity	left to right
NADH + NADP(+) + H(+)(out) => NAD(+) + NADPH + H(+)(in) `RHEA:47994`	molecular activity	right to left
NAD(+) + NADPH => NADH + NADP(+) `RHEA:11693`	molecular activity	left to right

Mechanistic edges

References

RHEA:18630 Rhea RHEA:18630: exact directional reaction (source version: Rhea142 issuing RDF; original selected direction/side/participant/containsN chains; pinned Rhea139 SQL separately supplies display label)
RHEA:28051 Rhea RHEA:28051: exact directional reaction (source version: Rhea142 issuing RDF; original selected direction/side/participant/containsN chains; pinned Rhea139 SQL separately supplies display label)
RHEA:47994 Rhea RHEA:47994: exact directional reaction (source version: Rhea142 issuing RDF; original selected direction/side/participant/containsN chains; pinned Rhea139 SQL separately supplies display label)
RHEA:11693 Rhea RHEA:11693: exact directional reaction (source version: Rhea142 issuing RDF; original selected direction/side/participant/containsN chains; pinned Rhea139 SQL separately supplies display label)
MetaCyc:NADPHOS-DEPHOS-PWY MetaCyc NADPHOS-DEPHOS-PWY: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:NAD-KIN-ENZRXN EcoCyc NAD-KIN-ENZRXN: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:ENZRXN0-7742 EcoCyc ENZRXN0-7742: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:PYRNUTRANSHYDROGEN-ENZRXN EcoCyc PYRNUTRANSHYDROGEN-ENZRXN: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:UDHA-ENZRXN EcoCyc UDHA-ENZRXN: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:CPLX0-682 EcoCyc CPLX0-682: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:MONOMER0-541 EcoCyc MONOMER0-541: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:ALKAPHOSPHA-CPLX EcoCyc ALKAPHOSPHA-CPLX: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:ALKAPHOSPHA-MONOMER EcoCyc ALKAPHOSPHA-MONOMER: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:PYRNUTRANSHYDROGEN-CPLX EcoCyc PYRNUTRANSHYDROGEN-CPLX: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:PNTA-MONOMER EcoCyc PNTA-MONOMER: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:PNTB-MONOMER EcoCyc PNTB-MONOMER: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:UDHA-CPLX EcoCyc UDHA-CPLX: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:UDHA-MONOMER EcoCyc UDHA-MONOMER: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
UniProtKB:P0A7B3 NAD kinase (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
Entrez:947092 nadK: issuing MG1655 Gene record (source version: Exact Entrezgene XML, GeneID, b-locus and taxon511145; retrieved2026-10-12)
UniProtKB:P00634 Alkaline phosphatase (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
Entrez:945041 phoA: issuing MG1655 Gene record (source version: Exact Entrezgene XML, GeneID, b-locus and taxon511145; retrieved2026-10-12)
UniProtKB:P07001 NAD(P) transhydrogenase subunit alpha (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
Entrez:946628 pntA: issuing MG1655 Gene record (source version: Exact Entrezgene XML, GeneID, b-locus and taxon511145; retrieved2026-10-12)
UniProtKB:P0AB67 NAD(P) transhydrogenase subunit beta (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
Entrez:946144 pntB: issuing MG1655 Gene record (source version: Exact Entrezgene XML, GeneID, b-locus and taxon511145; retrieved2026-10-12)
UniProtKB:P27306 Soluble pyridine nucleotide transhydrogenase (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
Entrez:948461 sthA: issuing MG1655 Gene record (source version: Exact Entrezgene XML, GeneID, b-locus and taxon511145; retrieved2026-10-12)
UniProtKB:P22255 3'(2'),5'-bisphosphate nucleotidase CysQ (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
Entrez:948728 cysQ: issuing MG1655 Gene record (source version: Exact Entrezgene XML, GeneID, b-locus and taxon511145; retrieved2026-10-12)
PMID:11488932 Molecular characterization of Escherichia coli NAD kinase. (source version: Primary-paper tool renderings bundled losslessly with exact original receipts; no raw publisher PDF/HTML claim)
PMID:3025169 Negative modulation of Escherichia coli NAD kinase by NADPH and NADH. (source version: Retained full primary original; exact preparation and inspected source locators; supplementary originals separately bound)
EcoCyc:REG0-7644 EcoCyc REG0-7644: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:REG0-7643 EcoCyc REG0-7643: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
PMID:13906598 A study of the substrate specificity and other properties of the alkaline phosphatase of Escherichia coli. (source version: Primary-paper tool renderings bundled losslessly with exact original receipts; no raw publisher PDF/HTML claim)
PMID:17616624 NADP(H) phosphatase activities of archaeal inositol monophosphatase and eubacterial 3'-phosphoadenosine 5'-phosphate phosphatase. (source version: Retained full primary original; exact preparation and inspected source locators; supplementary originals separately bound)
PMID:34707181 Energy transfer between the nicotinamide nucleotide transhydrogenase and ATP synthase of Escherichia coli. (source version: Retained full primary original; exact preparation and inspected source locators; supplementary originals separately bound)
PMID:3891338 Purification and properties of reconstitutively active nicotinamide nucleotide transhydrogenase of Escherichia coli. (source version: Primary abstract/metadata only; exact EuropePMC MED PMID selector, not full-body access)
EcoCyc:REG0-8848 EcoCyc REG0-8848: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
PMID:10556628 Effect of NBD chloride (4-chloro-7-nitrobenzo-2-oxa-1,3-diazole) on the pyridine nucleotide transhydrogenase of Escherichia coli. (source version: Primary abstract/metadata only; exact EuropePMC MED PMID selector, not full-body access)
EcoCyc:REG0-9666 EcoCyc REG0-9666: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
PMID:35933012 A conserved sequence motif in the Escherichia coli soluble FAD-containing pyridine nucleotide transhydrogenase is important for reaction efficiency. (source version: Retained full primary original; exact preparation and inspected source locators; supplementary originals separately bound)
DOI:10.1016/j.jbc.2022.102304 A conserved sequence motif in the Escherichia coli soluble FAD-containing pyridine nucleotide transhydrogenase is important for reaction efficiency. — original supplementary document (source version: Exact original supplementary DOCX; member word/document.xml SHA256 0317575d294ddc66cbe14e16d0fe5c95b47584b70df31eb60b7c0ff08fe39a49; separately bound from main paper)
PMID:21545646 Overexpression and biochemical characterization of soluble pyridine nucleotide transhydrogenase from Escherichia coli. (source version: Primary abstract/metadata only; exact EuropePMC MED PMID selector, not full-body access)
EcoCyc:PC00027 EcoCyc PC00027: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:PD00347 EcoCyc PD00347: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
UniProtKB:P0A6X7 Integration host factor subunit alpha (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
EcoCyc:PD00348 EcoCyc PD00348: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
UniProtKB:P0A6Y1 Integration host factor subunit beta (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
EcoCyc:CPLX0-226 EcoCyc CPLX0-226: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
UniProtKB:P0ACJ8 DNA-binding transcriptional dual regulator CRP (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
EcoCyc:PC00004 EcoCyc PC00004: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
PMID:27488847 Distinct transcriptional regulation of the two Escherichia coli transhydrogenases PntAB and UdhA. (source version: Retained full primary original; exact preparation and inspected source locators; supplementary originals separately bound)
UniProtKB:P0ACJ0 Leucine-responsive regulatory protein (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
UniProtKB:P0A8S1 HTH-type transcriptional regulator ArgP (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
UniProtKB:P0A9A9 Ferric uptake regulation protein (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
UniProtKB:P0A9Q1 Aerobic respiration control protein ArcA (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
UniProtKB:P0ACF8 DNA-binding protein H-NS (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
UniProtKB:P07604 HTH-type transcriptional regulatory protein TyrR (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
DOI:10.1099/mic.0.000346 Distinct transcriptional regulation of the two Escherichia coli transhydrogenases PntAB and UdhA. — original supplementary PDF (source version: Original supplemental PDF, source-qualified page/row selection; main paper separately bound)
PMID:30420454 Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes. (source version: Retained full primary original; exact preparation and inspected source locators; supplementary originals separately bound)
EcoCyc:REG0-15526 EcoCyc REG0-15526: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:PD00353 EcoCyc PD00353: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:REG0-15529 EcoCyc REG0-15529: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:REG0-15570 EcoCyc REG0-15570: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:PHOSPHO-ARCA EcoCyc PHOSPHO-ARCA: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
PMID:24699140 Determining the control circuitry of redox metabolism at the genome-scale. (source version: Retained full primary original; exact preparation and inspected source locators; supplementary originals separately bound)
EcoCyc:REG0-14088 EcoCyc REG0-14088: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:REG0-14089 EcoCyc REG0-14089: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:ARCA-MONOMER EcoCyc ARCA-MONOMER: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:REG0-14101 EcoCyc REG0-14101: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:REG0-14102 EcoCyc REG0-14102: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:REG0-14103 EcoCyc REG0-14103: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
PMID:28061857 Coordinated regulation of acid resistance in Escherichia coli. (source version: Retained full primary original; exact preparation and inspected source locators; supplementary originals separately bound)
DOI:10.1186/s12918-016-0376-y Coordinated regulation of acid resistance in Escherichia coli. — original supplementary archive (source version: Original supplementary ZIP; exact XLSX member SHA and worksheet/row retained separately)
EcoCyc:G7072-MONOMER EcoCyc G7072-MONOMER: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:REG0-11863 EcoCyc REG0-11863: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
PMID:21292161 The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli. (source version: Retained full primary original; exact preparation and inspected source locators; supplementary originals separately bound)
EcoCyc:PHOSPHO-PHOB EcoCyc PHOSPHO-PHOB: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:REG0-4617 EcoCyc REG0-4617: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:PM00071 EcoCyc PM00071: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:TU00052 EcoCyc TU00052: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
EcoCyc:PHOB-MONOMER EcoCyc PHOB-MONOMER: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
UniProtKB:P0AFJ5 Phosphate regulon transcriptional regulatory protein PhoB (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
UniProtKB:P37338 HTH-type transcriptional repressor GlaR (source version: Complete issuing UniProt JSON; exact accession, taxonomy, locus, sequence and entryAudit; retrieved2026-10-12)
PMID:8100227 Identification of N,N'-dicyclohexylcarbodiimide-reactive glutamic and aspartic acid residues in Escherichia coli transhydrogenase and the exchange of these by site-specific mutagenesis. (source version: Primary abstract/metadata only; exact EuropePMC MED PMID selector, not full-body access)
PMID:9922271 The udhA gene of Escherichia coli encodes a soluble pyridine nucleotide transhydrogenase. (source version: Primary abstract/metadata only; exact EuropePMC MED PMID selector, not full-body access)
PMID:15855156 Molecular conversion of NAD kinase to NADH kinase through single amino acid residue substitution. (source version: Primary abstract/metadata only; exact EuropePMC MED PMID selector, not full-body access)
PMID:23274360 Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant. (source version: Primary abstract/metadata only; exact EuropePMC MED PMID selector, not full-body access)
EcoCyc:NADPPHOSPHAT-MONOMER EcoCyc NADPPHOSPHAT-MONOMER: issuing native original (source version: PGDB27.0; unmodified native XML; retrieved2026-10-12; exact request/frame guards)
DOI:10.1371/journal.pgen.1004264.s009 ArcA supplementary table S1 (source version: Exact publisher supplemental PDF; separately acquired and bound; table context retained)
DOI:10.1371/journal.pgen.1004264.s010 ArcA supplementary table S2 (source version: Exact publisher supplemental PDF; separately acquired and bound; table context retained)
PathBank:SMP0002093 NAD phosphorylation and dephosphorylation — frozen PW002081 BioPAX (source version: Frozen archive member PW002081.owl SHA256 b6f8df0db6bf06cd671f3518481285f00b17d1eb384d8834826527c2201593e0; whole archive SHA256 b3a9b9557d4147fac0159d178a27c13cc1180729eae9ccb4fb32abebb1656f44; no live-download claim)
PMID:10383409 The membrane topology of proton-pumping Escherichia coli transhydrogenase determined by cysteine labeling. (source version: Primary abstract/metadata only; exact EuropePMC MED PMID selector, not full-body access)
PMID:14660605 The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli. (source version: Retained full primary original; narrative-only citation with exact paragraph/source accounting; not a new mechanistic edge or fresh retrieval)
PMID:30765722 Quantifying dynamic mechanisms of auto-regulation in Escherichia coli with synthetic promoter in response to varying external phosphate levels. (source version: Retained full primary original; narrative-only citation with exact paragraph/source accounting; not a new mechanistic edge or fresh retrieval)
PMID:22388518 Multiple factors dictate target selection by Hfq-binding small RNAs (source version: Retained full primary original; narrative-only citation with exact paragraph/source accounting; not a new mechanistic edge or fresh retrieval)

Curation history

2026-10-12T09:42:44Z codex
- CREATE — Add the NAD phosphorylation and dephosphorylation pathway
  Adopt the independently reviewed MetaCyc:NADPHOS-DEPHOS-PWY record, exact SHA-256 96e493c58ab830ec79f0e4ed4e49d68a9f4e49d761e62b58e86c8783a7a569c7, with three native core events and a separate supporting SthA event, 19 total reaction sides, 102 mechanistic edges, 48 endpoint qualifiers, 266 evidence uses and 97 references. Preserve the unknown physiological NADP phosphatase, proton-transport scope, exact protein/complex identity, organism, strain, construct, assay and source-access limits established in the complete original and bounded successor scientific reviews. Corrections for issues 465, 466, 468 and 469 and the authority relocation narrative correction for issue 467 retain their original evidence and dispositions in research/pathway_additions/2026-10-12-next-232. Adopt the actual native source/ontology outputs and all 11 new whole source originals, including the separate PC-1 class source, after binding the 232 prior records to actual merged PPi commit 19af3cc154dbbd757c17299b36923e5f9ccc31dc. This event records the actual maintained adoption before rendering; full maintained gates, preservation, page QA, native saved review and PR publication are subsequent steps, not outcomes claimed here.
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2026-10-12T11:21:34Z codex
- EDIT — Correct NAD inhibition assay context for issue 483.
  Adopt the independently accepted paragraph-7 successor: distinguish general 10 mM NAD Methods from Table 2 assays at 4.0 mM NAD and separate variable-NAD saturation experiments. Retain the supported inhibition/additivity and Hill/Km limits. Only this description paragraph and two active-ledger text pointers change; all other scientific structure and prior dossiers, history and native review 109 remain immutable. Exact author and independent review evidence is retained additively under research/pathway_additions/2026-10-12-next-232/assay-context-correction. This EDIT records adoption before rendering; maintained gates and the bounded native successor are recorded separately after actual execution.
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