L-lysine biosynthesis I

MetaCyc:DAPLYSINESYN-PWY

L-lysine biosynthesis I converts L-aspartate to L-lysine through L-aspartate 4-semialdehyde, cyclic tetrahydrodipicolinate intermediates, a succinylated diaminopimelate branch, and meso-2,6-diaminopimelate.

Pathway type

amino acid biosynthesis

Organism scope

Escherichia coli NCBITaxon:562

Read the source YAML

Pathway network

61 nodes · 90 asserted directed edges

Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.

Find a node

Reaction / activity
Chemical / cofactor
Protein / complex
Other participant
Cell / process context
Solid arrow: mechanistic relation
Dashed arrow: membership, location or cofactor relation

Show at full size (scroll to explore)

Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Escherichia coli `NCBITaxon:562`	taxon
aspartate kinase `EC:2.7.2.4`	molecular activity
aspartate-semialdehyde dehydrogenase `EC:1.2.1.11`	molecular activity
4-hydroxy-tetrahydrodipicolinate synthase `EC:4.3.3.7`	molecular activity
4-hydroxy-tetrahydrodipicolinate reductase `EC:1.17.1.8`	molecular activity
tetrahydrodipicolinate N-succinyltransferase `EC:2.3.1.117`	molecular activity
succinyldiaminopimelate transaminase `EC:2.6.1.17`	molecular activity
succinyl-diaminopimelate desuccinylase `EC:3.5.1.18`	molecular activity
diaminopimelate epimerase `EC:5.1.1.7`	molecular activity
diaminopimelate decarboxylase `EC:4.1.1.20`	molecular activity
L-aspartate `CHEBI:29991`	small molecule
ATP `CHEBI:30616`	small molecule
4-phospho-L-aspartate `CHEBI:57535`	small molecule
ADP `CHEBI:456216`	small molecule
NADPH `CHEBI:57783`	small molecule
H(+) `CHEBI:15378`	small molecule
L-aspartate 4-semialdehyde `CHEBI:537519`	small molecule
phosphate `CHEBI:43474`	small molecule
NADP(+) `CHEBI:58349`	small molecule
pyruvate `CHEBI:15361`	small molecule
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate `CHEBI:67139`	small molecule
H2O `CHEBI:15377`	small molecule
NADH `CHEBI:57945`	small molecule
(S)-2,3,4,5-tetrahydrodipicolinate `CHEBI:16845`	small molecule
NAD(+) `CHEBI:57540`	small molecule
succinyl-CoA `CHEBI:57292`	small molecule
(S)-2-succinylamino-6-oxoheptanedioate `CHEBI:15685`	small molecule
CoA `CHEBI:57287`	small molecule
L-glutamate `CHEBI:29985`	small molecule
N-succinyl-(2S,6S)-2,6-diaminopimelate `CHEBI:58087`	small molecule
2-oxoglutarate `CHEBI:16810`	small molecule
(2S,6S)-2,6-diaminopimelate `CHEBI:57609`	small molecule
succinate `CHEBI:30031`	small molecule
meso-2,6-diaminopimelate `CHEBI:57791`	small molecule
L-lysine `CHEBI:32551`	small molecule
CO2 `CHEBI:16526`	small molecule
Bifunctional aspartokinase/homoserine dehydrogenase 1 `UniProtKB:P00561`	protein
L-threonine zwitterion `CHEBI:57926`	small molecule
Bifunctional aspartokinase/homoserine dehydrogenase 2 `UniProtKB:P00562`	protein
Diaminopimelate decarboxylase `UniProtKB:P00861`	protein
pyridoxal 5'-phosphate(2-) `CHEBI:597326`	cofactor
4-hydroxy-tetrahydrodipicolinate reductase `UniProtKB:P04036`	protein
cytoplasm `GO:0005737`	cellular component
Lysine-sensitive aspartokinase 3 `UniProtKB:P08660`	protein
Diaminopimelate epimerase `UniProtKB:P0A6K1`	protein
4-hydroxy-tetrahydrodipicolinate synthase `UniProtKB:P0A6L2`	protein
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase `UniProtKB:P0A9D8`	protein
Aspartate-semialdehyde dehydrogenase `UniProtKB:P0A9Q9`	protein
Succinyl-diaminopimelate desuccinylase `UniProtKB:P0AED7`	protein
zinc(2+) `CHEBI:29105`	cofactor
cobalt(2+) `CHEBI:48828`	cofactor
Acetylornithine/succinyldiaminopimelate aminotransferase `UniProtKB:P18335`	protein
ATP-dependent aspartate kinase reaction `RHEA:23777`	reaction	left to right
NADPH-dependent aspartate-semialdehyde dehydrogenase reaction `RHEA:24286`	reaction	right to left
4-hydroxy-tetrahydrodipicolinate synthase reaction `RHEA:34172`	reaction	left to right
NADH-dependent dihydrodipicolinate reductase reaction `RHEA:35325`	reaction	right to left
NADPH-dependent dihydrodipicolinate reductase reaction `RHEA:35333`	reaction	right to left
tetrahydrodipicolinate N-succinyltransferase reaction `RHEA:17326`	reaction	left to right
N-succinyldiaminopimelate aminotransferase reaction `RHEA:11962`	reaction	right to left
N-succinyldiaminopimelate desuccinylase reaction `RHEA:22609`	reaction	left to right
diaminopimelate epimerase reaction `RHEA:15394`	reaction	left to right
diaminopimelate decarboxylase reaction `RHEA:15102`	reaction	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
L-aspartate `CHEBI:29991`	consumes	ATP-dependent aspartate kinase reaction `RHEA:23777`	RHEA:23777 Source assertion: Rhea lists CHEBI:29991 on the substrates side of RHEA:23777 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/23777']/rh:substrates; rh:contains/rh:compound/rh:accession`
ATP `CHEBI:30616`	consumes	ATP-dependent aspartate kinase reaction `RHEA:23777`	RHEA:23777 Source assertion: Rhea lists CHEBI:30616 on the substrates side of RHEA:23777 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/23777']/rh:substrates; rh:contains/rh:compound/rh:accession`
ATP-dependent aspartate kinase reaction `RHEA:23777`	produces	ADP `CHEBI:456216`	RHEA:23777 Source assertion: Rhea lists CHEBI:456216 on the products side of RHEA:23777 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/23777']/rh:products; rh:contains/rh:compound/rh:accession`
ATP-dependent aspartate kinase reaction `RHEA:23777`	produces	4-phospho-L-aspartate `CHEBI:57535`	RHEA:23777 Source assertion: Rhea lists CHEBI:57535 on the products side of RHEA:23777 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/23777']/rh:products; rh:contains/rh:compound/rh:accession`
H(+) `CHEBI:15378`	consumes	NADPH-dependent aspartate-semialdehyde dehydrogenase reaction `RHEA:24286`	RHEA:24286 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:24286 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/24286']/rh:substrates; rh:contains/rh:compound/rh:accession`
4-phospho-L-aspartate `CHEBI:57535`	consumes	NADPH-dependent aspartate-semialdehyde dehydrogenase reaction `RHEA:24286`	RHEA:24286 Source assertion: Rhea lists CHEBI:57535 on the substrates side of RHEA:24286 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/24286']/rh:substrates; rh:contains/rh:compound/rh:accession`
NADPH `CHEBI:57783`	consumes	NADPH-dependent aspartate-semialdehyde dehydrogenase reaction `RHEA:24286`	RHEA:24286 Source assertion: Rhea lists CHEBI:57783 on the substrates side of RHEA:24286 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/24286']/rh:substrates; rh:contains/rh:compound/rh:accession`
NADPH-dependent aspartate-semialdehyde dehydrogenase reaction `RHEA:24286`	produces	phosphate `CHEBI:43474`	RHEA:24286 Source assertion: Rhea lists CHEBI:43474 on the products side of RHEA:24286 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/24286']/rh:products; rh:contains/rh:compound/rh:accession`
NADPH-dependent aspartate-semialdehyde dehydrogenase reaction `RHEA:24286`	produces	L-aspartate 4-semialdehyde `CHEBI:537519`	RHEA:24286 Source assertion: Rhea lists CHEBI:537519 on the products side of RHEA:24286 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/24286']/rh:products; rh:contains/rh:compound/rh:accession`
NADPH-dependent aspartate-semialdehyde dehydrogenase reaction `RHEA:24286`	produces	NADP(+) `CHEBI:58349`	RHEA:24286 Source assertion: Rhea lists CHEBI:58349 on the products side of RHEA:24286 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/24286']/rh:products; rh:contains/rh:compound/rh:accession`
pyruvate `CHEBI:15361`	consumes	4-hydroxy-tetrahydrodipicolinate synthase reaction `RHEA:34172`	RHEA:34172 Source assertion: Rhea lists CHEBI:15361 on the substrates side of RHEA:34172 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/34172']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-aspartate 4-semialdehyde `CHEBI:537519`	consumes	4-hydroxy-tetrahydrodipicolinate synthase reaction `RHEA:34172`	RHEA:34172 Source assertion: Rhea lists CHEBI:537519 on the substrates side of RHEA:34172 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/34172']/rh:substrates; rh:contains/rh:compound/rh:accession`
4-hydroxy-tetrahydrodipicolinate synthase reaction `RHEA:34172`	produces	H2O `CHEBI:15377`	RHEA:34172 Source assertion: Rhea lists CHEBI:15377 on the products side of RHEA:34172 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/34172']/rh:products; rh:contains/rh:compound/rh:accession`
4-hydroxy-tetrahydrodipicolinate synthase reaction `RHEA:34172`	produces	H(+) `CHEBI:15378`	RHEA:34172 Source assertion: Rhea lists CHEBI:15378 on the products side of RHEA:34172 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/34172']/rh:products; rh:contains/rh:compound/rh:accession`
4-hydroxy-tetrahydrodipicolinate synthase reaction `RHEA:34172`	produces	(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate `CHEBI:67139`	RHEA:34172 Source assertion: Rhea lists CHEBI:67139 on the products side of RHEA:34172 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/34172']/rh:products; rh:contains/rh:compound/rh:accession`
H(+) `CHEBI:15378`	consumes	NADH-dependent dihydrodipicolinate reductase reaction `RHEA:35325`	RHEA:35325 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:35325 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/35325']/rh:substrates; rh:contains/rh:compound/rh:accession`
NADH `CHEBI:57945`	consumes	NADH-dependent dihydrodipicolinate reductase reaction `RHEA:35325`	RHEA:35325 Source assertion: Rhea lists CHEBI:57945 on the substrates side of RHEA:35325 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/35325']/rh:substrates; rh:contains/rh:compound/rh:accession`
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate `CHEBI:67139`	consumes	NADH-dependent dihydrodipicolinate reductase reaction `RHEA:35325`	RHEA:35325 Source assertion: Rhea lists CHEBI:67139 on the substrates side of RHEA:35325 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/35325']/rh:substrates; rh:contains/rh:compound/rh:accession`
NADH-dependent dihydrodipicolinate reductase reaction `RHEA:35325`	produces	H2O `CHEBI:15377`	RHEA:35325 Source assertion: Rhea lists CHEBI:15377 on the products side of RHEA:35325 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/35325']/rh:products; rh:contains/rh:compound/rh:accession`
NADH-dependent dihydrodipicolinate reductase reaction `RHEA:35325`	produces	(S)-2,3,4,5-tetrahydrodipicolinate `CHEBI:16845`	RHEA:35325 Source assertion: Rhea lists CHEBI:16845 on the products side of RHEA:35325 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/35325']/rh:products; rh:contains/rh:compound/rh:accession`
NADH-dependent dihydrodipicolinate reductase reaction `RHEA:35325`	produces	NAD(+) `CHEBI:57540`	RHEA:35325 Source assertion: Rhea lists CHEBI:57540 on the products side of RHEA:35325 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/35325']/rh:products; rh:contains/rh:compound/rh:accession`
H(+) `CHEBI:15378`	consumes	NADPH-dependent dihydrodipicolinate reductase reaction `RHEA:35333`	RHEA:35333 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:35333 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/35333']/rh:substrates; rh:contains/rh:compound/rh:accession`
NADPH `CHEBI:57783`	consumes	NADPH-dependent dihydrodipicolinate reductase reaction `RHEA:35333`	RHEA:35333 Source assertion: Rhea lists CHEBI:57783 on the substrates side of RHEA:35333 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/35333']/rh:substrates; rh:contains/rh:compound/rh:accession`
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate `CHEBI:67139`	consumes	NADPH-dependent dihydrodipicolinate reductase reaction `RHEA:35333`	RHEA:35333 Source assertion: Rhea lists CHEBI:67139 on the substrates side of RHEA:35333 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/35333']/rh:substrates; rh:contains/rh:compound/rh:accession`
NADPH-dependent dihydrodipicolinate reductase reaction `RHEA:35333`	produces	H2O `CHEBI:15377`	RHEA:35333 Source assertion: Rhea lists CHEBI:15377 on the products side of RHEA:35333 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/35333']/rh:products; rh:contains/rh:compound/rh:accession`
NADPH-dependent dihydrodipicolinate reductase reaction `RHEA:35333`	produces	(S)-2,3,4,5-tetrahydrodipicolinate `CHEBI:16845`	RHEA:35333 Source assertion: Rhea lists CHEBI:16845 on the products side of RHEA:35333 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/35333']/rh:products; rh:contains/rh:compound/rh:accession`
NADPH-dependent dihydrodipicolinate reductase reaction `RHEA:35333`	produces	NADP(+) `CHEBI:58349`	RHEA:35333 Source assertion: Rhea lists CHEBI:58349 on the products side of RHEA:35333 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/35333']/rh:products; rh:contains/rh:compound/rh:accession`
H2O `CHEBI:15377`	consumes	tetrahydrodipicolinate N-succinyltransferase reaction `RHEA:17326`	RHEA:17326 Source assertion: Rhea lists CHEBI:15377 on the substrates side of RHEA:17326 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17326']/rh:substrates; rh:contains/rh:compound/rh:accession`
(S)-2,3,4,5-tetrahydrodipicolinate `CHEBI:16845`	consumes	tetrahydrodipicolinate N-succinyltransferase reaction `RHEA:17326`	RHEA:17326 Source assertion: Rhea lists CHEBI:16845 on the substrates side of RHEA:17326 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17326']/rh:substrates; rh:contains/rh:compound/rh:accession`
succinyl-CoA `CHEBI:57292`	consumes	tetrahydrodipicolinate N-succinyltransferase reaction `RHEA:17326`	RHEA:17326 Source assertion: Rhea lists CHEBI:57292 on the substrates side of RHEA:17326 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17326']/rh:substrates; rh:contains/rh:compound/rh:accession`
tetrahydrodipicolinate N-succinyltransferase reaction `RHEA:17326`	produces	(S)-2-succinylamino-6-oxoheptanedioate `CHEBI:15685`	RHEA:17326 Source assertion: Rhea lists CHEBI:15685 on the products side of RHEA:17326 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17326']/rh:products; rh:contains/rh:compound/rh:accession`
tetrahydrodipicolinate N-succinyltransferase reaction `RHEA:17326`	produces	CoA `CHEBI:57287`	RHEA:17326 Source assertion: Rhea lists CHEBI:57287 on the products side of RHEA:17326 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17326']/rh:products; rh:contains/rh:compound/rh:accession`
(S)-2-succinylamino-6-oxoheptanedioate `CHEBI:15685`	consumes	N-succinyldiaminopimelate aminotransferase reaction `RHEA:11962`	RHEA:11962 Source assertion: Rhea lists CHEBI:15685 on the substrates side of RHEA:11962 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/11962']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-glutamate `CHEBI:29985`	consumes	N-succinyldiaminopimelate aminotransferase reaction `RHEA:11962`	RHEA:11962 Source assertion: Rhea lists CHEBI:29985 on the substrates side of RHEA:11962 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/11962']/rh:substrates; rh:contains/rh:compound/rh:accession`
N-succinyldiaminopimelate aminotransferase reaction `RHEA:11962`	produces	2-oxoglutarate `CHEBI:16810`	RHEA:11962 Source assertion: Rhea lists CHEBI:16810 on the products side of RHEA:11962 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/11962']/rh:products; rh:contains/rh:compound/rh:accession`
N-succinyldiaminopimelate aminotransferase reaction `RHEA:11962`	produces	N-succinyl-(2S,6S)-2,6-diaminopimelate `CHEBI:58087`	RHEA:11962 Source assertion: Rhea lists CHEBI:58087 on the products side of RHEA:11962 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/11962']/rh:products; rh:contains/rh:compound/rh:accession`
H2O `CHEBI:15377`	consumes	N-succinyldiaminopimelate desuccinylase reaction `RHEA:22609`	RHEA:22609 Source assertion: Rhea lists CHEBI:15377 on the substrates side of RHEA:22609 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22609']/rh:substrates; rh:contains/rh:compound/rh:accession`
N-succinyl-(2S,6S)-2,6-diaminopimelate `CHEBI:58087`	consumes	N-succinyldiaminopimelate desuccinylase reaction `RHEA:22609`	RHEA:22609 Source assertion: Rhea lists CHEBI:58087 on the substrates side of RHEA:22609 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22609']/rh:substrates; rh:contains/rh:compound/rh:accession`
N-succinyldiaminopimelate desuccinylase reaction `RHEA:22609`	produces	succinate `CHEBI:30031`	RHEA:22609 Source assertion: Rhea lists CHEBI:30031 on the products side of RHEA:22609 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22609']/rh:products; rh:contains/rh:compound/rh:accession`
N-succinyldiaminopimelate desuccinylase reaction `RHEA:22609`	produces	(2S,6S)-2,6-diaminopimelate `CHEBI:57609`	RHEA:22609 Source assertion: Rhea lists CHEBI:57609 on the products side of RHEA:22609 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22609']/rh:products; rh:contains/rh:compound/rh:accession`
(2S,6S)-2,6-diaminopimelate `CHEBI:57609`	consumes	diaminopimelate epimerase reaction `RHEA:15394`	RHEA:15394 Source assertion: Rhea lists CHEBI:57609 on the substrates side of RHEA:15394 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/15394']/rh:substrates; rh:contains/rh:compound/rh:accession`
diaminopimelate epimerase reaction `RHEA:15394`	produces	meso-2,6-diaminopimelate `CHEBI:57791`	RHEA:15394 Source assertion: Rhea lists CHEBI:57791 on the products side of RHEA:15394 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/15394']/rh:products; rh:contains/rh:compound/rh:accession`
H(+) `CHEBI:15378`	consumes	diaminopimelate decarboxylase reaction `RHEA:15102`	RHEA:15102 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:15102 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/15102']/rh:substrates; rh:contains/rh:compound/rh:accession`
meso-2,6-diaminopimelate `CHEBI:57791`	consumes	diaminopimelate decarboxylase reaction `RHEA:15102`	RHEA:15102 Source assertion: Rhea lists CHEBI:57791 on the substrates side of RHEA:15102 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/15102']/rh:substrates; rh:contains/rh:compound/rh:accession`
diaminopimelate decarboxylase reaction `RHEA:15102`	produces	CO2 `CHEBI:16526`	RHEA:15102 Source assertion: Rhea lists CHEBI:16526 on the products side of RHEA:15102 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/15102']/rh:products; rh:contains/rh:compound/rh:accession`
diaminopimelate decarboxylase reaction `RHEA:15102`	produces	L-lysine `CHEBI:32551`	RHEA:15102 Source assertion: Rhea lists CHEBI:32551 on the products side of RHEA:15102 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/15102']/rh:products; rh:contains/rh:compound/rh:accession`
aspartate kinase `EC:2.7.2.4`	catalyzes	ATP-dependent aspartate kinase reaction `RHEA:23777`	RHEA:23776 Source assertion: Rhea associates EC:2.7.2.4 with the reaction family containing RHEA:23777. Source location `rh:ec`
aspartate-semialdehyde dehydrogenase `EC:1.2.1.11`	catalyzes	NADPH-dependent aspartate-semialdehyde dehydrogenase reaction `RHEA:24286`	RHEA:24284 Source assertion: Rhea associates EC:1.2.1.11 with the reaction family containing RHEA:24286. Source location `rh:ec`
4-hydroxy-tetrahydrodipicolinate synthase `EC:4.3.3.7`	catalyzes	4-hydroxy-tetrahydrodipicolinate synthase reaction `RHEA:34172`	RHEA:34171 Source assertion: Rhea associates EC:4.3.3.7 with the reaction family containing RHEA:34172. Source location `rh:ec`
4-hydroxy-tetrahydrodipicolinate reductase `EC:1.17.1.8`	catalyzes	NADH-dependent dihydrodipicolinate reductase reaction `RHEA:35325`	RHEA:35323 Source assertion: Rhea associates EC:1.17.1.8 with the reaction family containing RHEA:35325. Source location `rh:ec`
4-hydroxy-tetrahydrodipicolinate reductase `EC:1.17.1.8`	catalyzes	NADPH-dependent dihydrodipicolinate reductase reaction `RHEA:35333`	RHEA:35331 Source assertion: Rhea associates EC:1.17.1.8 with the reaction family containing RHEA:35333. Source location `rh:ec`
tetrahydrodipicolinate N-succinyltransferase `EC:2.3.1.117`	catalyzes	tetrahydrodipicolinate N-succinyltransferase reaction `RHEA:17326`	RHEA:17325 Source assertion: Rhea associates EC:2.3.1.117 with the reaction family containing RHEA:17326. Source location `rh:ec`
succinyldiaminopimelate transaminase `EC:2.6.1.17`	catalyzes	N-succinyldiaminopimelate aminotransferase reaction `RHEA:11962`	RHEA:11960 Source assertion: Rhea associates EC:2.6.1.17 with the reaction family containing RHEA:11962. Source location `rh:ec`
succinyl-diaminopimelate desuccinylase `EC:3.5.1.18`	catalyzes	N-succinyldiaminopimelate desuccinylase reaction `RHEA:22609`	RHEA:22608 Source assertion: Rhea associates EC:3.5.1.18 with the reaction family containing RHEA:22609. Source location `rh:ec`
diaminopimelate epimerase `EC:5.1.1.7`	catalyzes	diaminopimelate epimerase reaction `RHEA:15394`	RHEA:15393 Source assertion: Rhea associates EC:5.1.1.7 with the reaction family containing RHEA:15394. Source location `rh:ec`
diaminopimelate decarboxylase `EC:4.1.1.20`	catalyzes	diaminopimelate decarboxylase reaction `RHEA:15102`	RHEA:15101 Source assertion: Rhea associates EC:4.1.1.20 with the reaction family containing RHEA:15102. Source location `rh:ec`
N-succinyldiaminopimelate aminotransferase reaction `RHEA:11962`	precedes	N-succinyldiaminopimelate desuccinylase reaction `RHEA:22609`	MetaCyc:DAPLYSINESYN-PWY Source assertion: MetaCyc pathway ordering places RHEA:11962 before RHEA:22609 in this pathway. Shared intermediate: CHEBI:58087. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
diaminopimelate epimerase reaction `RHEA:15394`	precedes	diaminopimelate decarboxylase reaction `RHEA:15102`	MetaCyc:DAPLYSINESYN-PWY Source assertion: MetaCyc pathway ordering places RHEA:15394 before RHEA:15102 in this pathway. Shared intermediate: CHEBI:57791. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
tetrahydrodipicolinate N-succinyltransferase reaction `RHEA:17326`	precedes	N-succinyldiaminopimelate aminotransferase reaction `RHEA:11962`	MetaCyc:DAPLYSINESYN-PWY Source assertion: MetaCyc pathway ordering places RHEA:17326 before RHEA:11962 in this pathway. Shared intermediate: CHEBI:15685. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
N-succinyldiaminopimelate desuccinylase reaction `RHEA:22609`	precedes	diaminopimelate epimerase reaction `RHEA:15394`	MetaCyc:DAPLYSINESYN-PWY Source assertion: MetaCyc pathway ordering places RHEA:22609 before RHEA:15394 in this pathway. Shared intermediate: CHEBI:57609. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
ATP-dependent aspartate kinase reaction `RHEA:23777`	precedes	NADPH-dependent aspartate-semialdehyde dehydrogenase reaction `RHEA:24286`	MetaCyc:DAPLYSINESYN-PWY Source assertion: MetaCyc pathway ordering places RHEA:23777 before RHEA:24286 in this pathway. Shared intermediate: CHEBI:57535. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
NADPH-dependent aspartate-semialdehyde dehydrogenase reaction `RHEA:24286`	precedes	4-hydroxy-tetrahydrodipicolinate synthase reaction `RHEA:34172`	MetaCyc:DAPLYSINESYN-PWY Source assertion: MetaCyc pathway ordering places RHEA:24286 before RHEA:34172 in this pathway. Shared intermediate: CHEBI:537519. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
4-hydroxy-tetrahydrodipicolinate synthase reaction `RHEA:34172`	precedes	NADH-dependent dihydrodipicolinate reductase reaction `RHEA:35325`	MetaCyc:DAPLYSINESYN-PWY Source assertion: MetaCyc pathway ordering places RHEA:34172 before RHEA:35325 in this pathway. Shared intermediate: CHEBI:67139. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
4-hydroxy-tetrahydrodipicolinate synthase reaction `RHEA:34172`	precedes	NADPH-dependent dihydrodipicolinate reductase reaction `RHEA:35333`	MetaCyc:DAPLYSINESYN-PWY Source assertion: MetaCyc pathway ordering places RHEA:34172 before RHEA:35333 in this pathway. Shared intermediate: CHEBI:67139. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
NADH-dependent dihydrodipicolinate reductase reaction `RHEA:35325`	precedes	tetrahydrodipicolinate N-succinyltransferase reaction `RHEA:17326`	MetaCyc:DAPLYSINESYN-PWY Source assertion: MetaCyc pathway ordering places RHEA:35325 before RHEA:17326 in this pathway. Shared intermediate: CHEBI:16845. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
NADPH-dependent dihydrodipicolinate reductase reaction `RHEA:35333`	precedes	tetrahydrodipicolinate N-succinyltransferase reaction `RHEA:17326`	MetaCyc:DAPLYSINESYN-PWY Source assertion: MetaCyc pathway ordering places RHEA:35333 before RHEA:17326 in this pathway. Shared intermediate: CHEBI:16845. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
Bifunctional aspartokinase/homoserine dehydrogenase 1 `UniProtKB:P00561`	enables	ATP-dependent aspartate kinase reaction `RHEA:23777`	UniProtKB:P00561 Source assertion: UniProt annotates UniProtKB:P00561 with catalytic activity for the reaction family of RHEA:23777. Annotation evidence: ECO:0000250; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
L-threonine zwitterion `CHEBI:57926`	regulates	Bifunctional aspartokinase/homoserine dehydrogenase 1 `UniProtKB:P00561`	UniProtKB:P00561 Source assertion: UniProt activity-regulation annotation: The enzyme activities are regulated allosterically by L-threonine Source location `comments[commentType='ACTIVITY REGULATION'].texts`
Bifunctional aspartokinase/homoserine dehydrogenase 2 `UniProtKB:P00562`	enables	ATP-dependent aspartate kinase reaction `RHEA:23777`	UniProtKB:P00562 Source assertion: UniProt annotates UniProtKB:P00562 with catalytic activity for the reaction family of RHEA:23777. Annotation evidence: ECO:0000250; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Diaminopimelate decarboxylase `UniProtKB:P00861`	enables	diaminopimelate decarboxylase reaction `RHEA:15102`	UniProtKB:P00861 Source assertion: UniProt annotates UniProtKB:P00861 with catalytic activity for the reaction family of RHEA:15102. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Diaminopimelate decarboxylase `UniProtKB:P00861`	has_cofactor	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:P00861 Source assertion: UniProt lists CHEBI:597326 as a cofactor of UniProtKB:P00861 (evidence: ECO:0000269). Source location `comments[commentType='COFACTOR'].cofactors and note`
4-hydroxy-tetrahydrodipicolinate reductase `UniProtKB:P04036`	enables	NADH-dependent dihydrodipicolinate reductase reaction `RHEA:35325`	UniProtKB:P04036 Source assertion: UniProt annotates UniProtKB:P04036 with catalytic activity for the reaction family of RHEA:35325. Annotation evidence: ECO:0000255, ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
4-hydroxy-tetrahydrodipicolinate reductase `UniProtKB:P04036`	enables	NADPH-dependent dihydrodipicolinate reductase reaction `RHEA:35333`	UniProtKB:P04036 Source assertion: UniProt annotates UniProtKB:P04036 with catalytic activity for the reaction family of RHEA:35333. Annotation evidence: ECO:0000255, ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
4-hydroxy-tetrahydrodipicolinate reductase `UniProtKB:P04036`	located_in	cytoplasm `GO:0005737`	UniProtKB:P04036 Source assertion: UniProt locates UniProtKB:P04036 in Cytoplasm (SL-0086, mapped by UniProt to GO:0005737). Annotation evidence: curated source annotation. Source location `comments[commentType='SUBCELLULAR LOCATION'].subcellularLocations; UniProt location vocabulary GO mapping`
Lysine-sensitive aspartokinase 3 `UniProtKB:P08660`	enables	ATP-dependent aspartate kinase reaction `RHEA:23777`	UniProtKB:P08660 Source assertion: UniProt annotates UniProtKB:P08660 with catalytic activity for the reaction family of RHEA:23777. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
L-lysine `CHEBI:32551`	inhibits	Lysine-sensitive aspartokinase 3 `UniProtKB:P08660`	UniProtKB:P08660 Source assertion: UniProt activity-regulation annotation: Synthesis and activity are sensitive to the allosteric inhibitor lysine, one of the end metabolites of the aspartic acid family branched pathway Source location `comments[commentType='ACTIVITY REGULATION'].texts`
Diaminopimelate epimerase `UniProtKB:P0A6K1`	enables	diaminopimelate epimerase reaction `RHEA:15394`	UniProtKB:P0A6K1 Source assertion: UniProt annotates UniProtKB:P0A6K1 with catalytic activity for the reaction family of RHEA:15394. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Diaminopimelate epimerase `UniProtKB:P0A6K1`	located_in	cytoplasm `GO:0005737`	UniProtKB:P0A6K1 Source assertion: UniProt locates UniProtKB:P0A6K1 in Cytoplasm (SL-0086, mapped by UniProt to GO:0005737). Annotation evidence: ECO:0000305. Source location `comments[commentType='SUBCELLULAR LOCATION'].subcellularLocations; UniProt location vocabulary GO mapping`
4-hydroxy-tetrahydrodipicolinate synthase `UniProtKB:P0A6L2`	enables	4-hydroxy-tetrahydrodipicolinate synthase reaction `RHEA:34172`	UniProtKB:P0A6L2 Source assertion: UniProt annotates UniProtKB:P0A6L2 with catalytic activity for the reaction family of RHEA:34172. Annotation evidence: ECO:0000255, ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
L-lysine `CHEBI:32551`	inhibits	4-hydroxy-tetrahydrodipicolinate synthase `UniProtKB:P0A6L2`	UniProtKB:P0A6L2 Source assertion: UniProt activity-regulation annotation: Is allosterically regulated by the feedback inhibitor (S)-lysine. Is inhibited by pyruvate analogs such as 3-fluoropyruvate, 2-ketobutyrate, glyoxylate, and beta-hydroxypyruvate. Is not inhibited by its substrate, (S)-ASA Source location `comments[commentType='ACTIVITY REGULATION'].texts`
4-hydroxy-tetrahydrodipicolinate synthase `UniProtKB:P0A6L2`	located_in	cytoplasm `GO:0005737`	UniProtKB:P0A6L2 Source assertion: UniProt locates UniProtKB:P0A6L2 in Cytoplasm (SL-0086, mapped by UniProt to GO:0005737). Annotation evidence: curated source annotation. Source location `comments[commentType='SUBCELLULAR LOCATION'].subcellularLocations; UniProt location vocabulary GO mapping`
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase `UniProtKB:P0A9D8`	enables	tetrahydrodipicolinate N-succinyltransferase reaction `RHEA:17326`	UniProtKB:P0A9D8 Source assertion: UniProt annotates UniProtKB:P0A9D8 with catalytic activity for the reaction family of RHEA:17326. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase `UniProtKB:P0A9D8`	located_in	cytoplasm `GO:0005737`	UniProtKB:P0A9D8 Source assertion: UniProt locates UniProtKB:P0A9D8 in Cytoplasm (SL-0086, mapped by UniProt to GO:0005737). Annotation evidence: curated source annotation. Source location `comments[commentType='SUBCELLULAR LOCATION'].subcellularLocations; UniProt location vocabulary GO mapping`
Aspartate-semialdehyde dehydrogenase `UniProtKB:P0A9Q9`	enables	NADPH-dependent aspartate-semialdehyde dehydrogenase reaction `RHEA:24286`	UniProtKB:P0A9Q9 Source assertion: UniProt annotates UniProtKB:P0A9Q9 with catalytic activity for the reaction family of RHEA:24286. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Succinyl-diaminopimelate desuccinylase `UniProtKB:P0AED7`	enables	N-succinyldiaminopimelate desuccinylase reaction `RHEA:22609`	UniProtKB:P0AED7 Source assertion: UniProt annotates UniProtKB:P0AED7 with catalytic activity for the reaction family of RHEA:22609. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Succinyl-diaminopimelate desuccinylase `UniProtKB:P0AED7`	has_cofactor	zinc(2+) `CHEBI:29105`	UniProtKB:P0AED7 Source assertion: UniProt lists CHEBI:29105 as a cofactor of UniProtKB:P0AED7 (evidence: ECO:0000269). Binds 2 Zn(2+) or Co(2+) ions per subunit. Source location `comments[commentType='COFACTOR'].cofactors and note`
Succinyl-diaminopimelate desuccinylase `UniProtKB:P0AED7`	has_cofactor	cobalt(2+) `CHEBI:48828`	UniProtKB:P0AED7 Source assertion: UniProt lists CHEBI:48828 as a cofactor of UniProtKB:P0AED7 (evidence: ECO:0000269). Binds 2 Zn(2+) or Co(2+) ions per subunit. Source location `comments[commentType='COFACTOR'].cofactors and note`
Acetylornithine/succinyldiaminopimelate aminotransferase `UniProtKB:P18335`	enables	N-succinyldiaminopimelate aminotransferase reaction `RHEA:11962`	UniProtKB:P18335 Source assertion: UniProt annotates UniProtKB:P18335 with catalytic activity for the reaction family of RHEA:11962. Annotation evidence: ECO:0000255, ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Acetylornithine/succinyldiaminopimelate aminotransferase `UniProtKB:P18335`	located_in	cytoplasm `GO:0005737`	UniProtKB:P18335 Source assertion: UniProt locates UniProtKB:P18335 in Cytoplasm (SL-0086, mapped by UniProt to GO:0005737). Annotation evidence: ECO:0000255, ECO:0000305. Source location `comments[commentType='SUBCELLULAR LOCATION'].subcellularLocations; UniProt location vocabulary GO mapping`
Acetylornithine/succinyldiaminopimelate aminotransferase `UniProtKB:P18335`	has_cofactor	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:P18335 Source assertion: UniProt lists CHEBI:597326 as a cofactor of UniProtKB:P18335 (evidence: ECO:0000255, ECO:0000305). Binds 1 pyridoxal phosphate per subunit. Source location `comments[commentType='COFACTOR'].cofactors and note`

References

MetaCyc:DAPLYSINESYN-PWY MetaCyc L-lysine biosynthesis I pathway (source version: 22.5)
RHEA:23776 Rhea aspartate kinase reaction (source version: 139)
RHEA:23777 Rhea L-aspartyl-4-phosphate-forming aspartate kinase direction (source version: 139)
RHEA:24284 Rhea aspartate-semialdehyde dehydrogenase reaction (source version: 139)
RHEA:24286 Rhea biosynthetic aspartate-semialdehyde dehydrogenase direction (source version: 139)
RHEA:34171 Rhea 4-hydroxy-tetrahydrodipicolinate synthase reaction (source version: 139)
RHEA:34172 Rhea 4-hydroxy-tetrahydrodipicolinate-forming direction (source version: 139)
RHEA:35323 Rhea NADH-dependent dihydrodipicolinate reductase reaction (source version: 139)
RHEA:35325 Rhea NADH-dependent tetrahydrodipicolinate-forming direction (source version: 139)
RHEA:35331 Rhea NADPH-dependent dihydrodipicolinate reductase reaction (source version: 139)
RHEA:35333 Rhea NADPH-dependent tetrahydrodipicolinate-forming direction (source version: 139)
RHEA:17325 Rhea tetrahydrodipicolinate N-succinyltransferase reaction (source version: 139)
RHEA:17326 Rhea N-succinylamino-6-oxoheptanedioate-forming direction (source version: 139)
RHEA:11960 Rhea succinyldiaminopimelate transaminase reaction (source version: 139)
RHEA:11962 Rhea N-succinyldiaminopimelate-forming transaminase direction (source version: 139)
RHEA:22608 Rhea succinyl-diaminopimelate desuccinylase reaction (source version: 139)
RHEA:22609 Rhea L,L-diaminopimelate-forming desuccinylase direction (source version: 139)
RHEA:15393 Rhea diaminopimelate epimerase reaction (source version: 139)
RHEA:15394 Rhea meso-diaminopimelate-forming epimerase direction (source version: 139)
RHEA:15101 Rhea diaminopimelate decarboxylase reaction (source version: 139)
RHEA:15102 Rhea L-lysine-forming diaminopimelate decarboxylase direction (source version: 139)
UniProtKB:P00561 UniProtKB:P00561 authority record (source version: 2026_03)
UniProtKB:P00562 UniProtKB:P00562 authority record (source version: 2026_03)
UniProtKB:P00861 UniProtKB:P00861 authority record (source version: 2026_03)
UniProtKB:P04036 UniProtKB:P04036 authority record (source version: 2026_03)
UniProtKB:P08660 UniProtKB:P08660 authority record (source version: 2026_03)
UniProtKB:P0A6K1 UniProtKB:P0A6K1 authority record (source version: 2026_03)
UniProtKB:P0A6L2 UniProtKB:P0A6L2 authority record (source version: 2026_03)
UniProtKB:P0A9D8 UniProtKB:P0A9D8 authority record (source version: 2026_03)
UniProtKB:P0A9Q9 UniProtKB:P0A9Q9 authority record (source version: 2026_03)
UniProtKB:P0AED7 UniProtKB:P0AED7 authority record (source version: 2026_03)
UniProtKB:P18335 UniProtKB:P18335 authority record (source version: 2026_03)

Curation history

2026-10-05T06:25:52Z codex
- EDIT — Review causal chemistry and add sourced molecular context
  Reviewed the entire record against MetaCyc 22.5 native pathway XML (including nested pathways), Rhea 139 explicit sides and directions, ENZYME 02-Sep-2026, PubMed records, and reviewed UniProt 2026_03 annotations within the record's taxon scope. Replaced generated structured-source quotations with source_assertion and source_locator. Typed molecular activities and participants. Reaction count 10 to 10; 0 directed-ID corrections; 11 protein annotations, 4 cofactor annotations and 5 sourced locations. All Rhea reaction substrate/product sets checked against independent Rhea authority; native pathway leaf coverage and source exceptions recorded in reports/causal_graph_review/metacyc-review.json. Full source URLs, versions and byte hashes are in metacyc-sources.json. All 50 MetaCyc records passed native schema validation; six targeted chemistry/evidence regression tests passed. Missing protein or cofactor annotations are not treated as biological absence; qualifications and exclusions are preserved in the ledger. Tentative sodium/metal-cation crystal-binding annotations for P00561/P00562 were excluded from has_cofactor assertions.
Read this curation session