propanediol degradation polyhedral organelle

GO:0031472 · Microcompartment · Protein shelled organelle · Proposed

An organelle found in bacteria consisting of a proteinaceous coat containing enzymes for the degradation of 1,2-propanediol whose purpose is the protection of the rest of the cell from the toxic propionaldehyde product of the enzyme diol dehydratase. [GO:0031472]

Synonyms: Pdu microcompartment; propanediol-utilizing metabolosome

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Essential	Role
Pdu BMC-H shell proteins	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	pduA, pduJ, pduK	CONDITIONAL	BMC-domain shell proteins that make the major hexameric tiles of the propanediol-utilization microcompartment. `DOI:10.1128/JB.184.5.1253-1261.2002` Havemann et al. showed that PduA is a shell protein required for normal polyhedral organelle formation in Salmonella. `DOI:10.1128/JB.185.17.5086-5095.2003` Havemann and Bobik purified Salmonella Pdu polyhedral organelles and detected PduA and PduJ as organelle components. `DOI:10.1038/s41467-020-15888-4` Yang et al. quantified the absolute abundance and organization of Pdu shell proteins in native Salmonella metabolosomes.
Pdu BMC-T shell proteins	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	pduB, pduT, pduU	CONDITIONAL	Tandem or circularly permuted BMC-domain shell proteins that tile the Pdu shell and contribute pores and shell-cargo contacts. `DOI:10.1128/JB.185.17.5086-5095.2003` Havemann and Bobik detected PduB and PduU in the purified Pdu organelle fraction. `DOI:10.1038/s41467-022-30608-w` Yang et al. connected the PduB N terminus with shell-cargo assembly during Pdu metabolosome biogenesis.
PduN BMC-P vertex shell protein	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	pduN	UNKNOWN	Pentameric shell protein that occupies vertices of the polyhedral Pdu shell. `DOI:10.1002/pro.2246` Wheatley et al. identified PduN as a pentameric vertex protein of the Pdu microcompartment shell. `DOI:10.1038/s41467-020-15888-4` Yang et al. include PduN among the quantified structural shell proteins of native Salmonella Pdu metabolosomes.
PduM structural protein	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	pduM	UNKNOWN	Structural protein that promotes coupling between the Pdu enzyme core and the closing shell during metabolosome biogenesis. `DOI:10.1128/JB.06529-11` Sinha et al. identified PduM as a structural component of the Salmonella 1,2-propanediol microcompartment. `DOI:10.1038/s41467-022-30608-w` Yang et al. placed PduM in the shell-cargo assembly pathway that builds the native Pdu metabolosome.
PduCDE diol dehydratase	Protein complex	part of	Reviewed label only (reviewed name; no accession asserted)	pduC, pduD, pduE	DISPENSABLE	Encapsulated cobalamin-dependent dehydratase that converts 1,2-propanediol to propionaldehyde in the lumen. `DOI:10.1128/JB.179.21.6633-6639.1997` Bobik et al. showed that pduCDE encode the three subunits necessary and sufficient for propanediol dehydratase activity in Salmonella. `DOI:10.1128/JB.05661-11` Fan and Bobik showed that the PduD N-terminal region packages PduCDE into the Pdu microcompartment.

Organism-specific protein examples

Named proteins in which each component's role was established, with the organism the evidence comes from. The component above is the taxon-agnostic family; these are the specific entries behind it.

Pdu BMC-H shell proteins

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P0A1C7`	Bacterial microcompartment shell protein PduA	pduA	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (`NCBITaxon:99287`)	REVIEWED
Role and evidence (3 references) The single reviewed UniProtKB entry for gene pduA in Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, a taxon this record names. Identifier for the component's declared gene symbol; it is not itself evidence that the protein is part of this structure. `PMID:11844753` Havemann GD et al. 2002, ‘PduA is a shell protein of polyhedral organelles involved in coenzyme B(12)-dependent degradation of 1,2-propanediol in Salmonella enterica serovar typhimurium LT2.’, J Bacteriol. ECO:0000269 experimental evidence cited by UniProt for the 'Bacterial microcompartment' localisation of P0A1C7. `PMID:12923081` Havemann GD et al. 2003, ‘Protein content of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar Typhimurium LT2.’, J Bacteriol. ECO:0000269 experimental evidence cited by UniProt for the 'Bacterial microcompartment' localisation of P0A1C7. `PMID:24747050` Sinha S et al. 2014, ‘Alanine scanning mutagenesis identifies an asparagine-arginine-lysine triad essential to assembly of the shell of the Pdu microcompartment.’, J Mol Biol. ECO:0000269 experimental evidence cited by UniProt for the 'Bacterial microcompartment' localisation of P0A1C7.
`UniProtKB:H9L478`	Bacterial microcompartment shell protein PduJ	pduJ	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (`NCBITaxon:99287`)	REVIEWED
Role and evidence (2 references) The single reviewed UniProtKB entry for gene pduJ in Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, a taxon this record names. Identifier for the component's declared gene symbol; it is not itself evidence that the protein is part of this structure. `PMID:12923081` Havemann GD et al. 2003, ‘Protein content of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar Typhimurium LT2.’, J Bacteriol. ECO:0000269 experimental evidence cited by UniProt for the 'Bacterial microcompartment' localisation of H9L478. `PMID:24747050` Sinha S et al. 2014, ‘Alanine scanning mutagenesis identifies an asparagine-arginine-lysine triad essential to assembly of the shell of the Pdu microcompartment.’, J Mol Biol. ECO:0000269 experimental evidence cited by UniProt for the 'Bacterial microcompartment' localisation of H9L478.
`UniProtKB:Q9XDN6`	Bacterial microcompartment shell protein PduK	pduK	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (`NCBITaxon:99287`)	REVIEWED
Role and evidence (1 reference) The single reviewed UniProtKB entry for gene pduK in Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, a taxon this record names. Identifier for the component's declared gene symbol; it is not itself evidence that the protein is part of this structure. `PMID:12923081` Havemann GD et al. 2003, ‘Protein content of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar Typhimurium LT2.’, J Bacteriol. ECO:0000269 experimental evidence cited by UniProt for the 'Bacterial microcompartment' localisation of Q9XDN6.

Pdu BMC-T shell proteins

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P37449`	Bacterial microcompartment shell protein PduB	pduB	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (`NCBITaxon:99287`)	REVIEWED
Role and evidence (2 references) The single reviewed UniProtKB entry for gene pduB in Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, a taxon this record names. Identifier for the component's declared gene symbol; it is not itself evidence that the protein is part of this structure. `PMID:12923081` Havemann GD et al. 2003, ‘Protein content of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar Typhimurium LT2.’, J Bacteriol. ECO:0000269 experimental evidence cited by UniProt for the 'Bacterial microcompartment' localisation of P37449. `PMID:27063436` Held M et al. 2016, ‘Engineering formation of multiple recombinant Eut protein nanocompartments in E. coli.’, Sci Rep. ECO:0000269 experimental evidence cited by UniProt for the 'Bacterial microcompartment' localisation of P37449.
`UniProtKB:Q9XDM8`	Bacterial microcompartment shell protein PduT	pduT	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (`NCBITaxon:99287`)	REVIEWED
Role and evidence (1 reference) The single reviewed UniProtKB entry for gene pduT in Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, a taxon this record names. Identifier for the component's declared gene symbol; it is not itself evidence that the protein is part of this structure. `PMID:12923081` Havemann GD et al. 2003, ‘Protein content of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar Typhimurium LT2.’, J Bacteriol. ECO:0000269 experimental evidence cited by UniProt for the 'Bacterial microcompartment' localisation of Q9XDM8.
`UniProtKB:P0A1D1`	Bacterial microcompartment shell protein PduU	pduU	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (`NCBITaxon:99287`)	REVIEWED
Role and evidence (2 references) The single reviewed UniProtKB entry for gene pduU in Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, a taxon this record names. Identifier for the component's declared gene symbol; it is not itself evidence that the protein is part of this structure. `PMID:12923081` Havemann GD et al. 2003, ‘Protein content of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar Typhimurium LT2.’, J Bacteriol. ECO:0000269 experimental evidence cited by UniProt for the 'Bacterial microcompartment' localisation of P0A1D1. `PMID:27063436` Held M et al. 2016, ‘Engineering formation of multiple recombinant Eut protein nanocompartments in E. coli.’, Sci Rep. ECO:0000269 experimental evidence cited by UniProt for the 'Bacterial microcompartment' localisation of P0A1D1.

PduN BMC-P vertex shell protein

Accession	Protein	Gene	Organism	Entry
`UniProtKB:Q9XDN3`	Bacterial microcompartment shell vertex protein PduN	pduN	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (`NCBITaxon:99287`)	REVIEWED
Role and evidence (1 reference) The single reviewed UniProtKB entry for gene pduN in Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, a taxon this record names. Identifier for the component's declared gene symbol; it is not itself evidence that the protein is part of this structure. `PMID:21239588` Cheng S et al. 2011, ‘Genetic analysis of the protein shell of the microcompartments involved in coenzyme B12-dependent 1,2-propanediol degradation by Salmonella.’, J Bacteriol. ECO:0000269 experimental evidence cited by UniProt for the 'Bacterial microcompartment' localisation of Q9XDN3.

PduM structural protein

Accession	Protein	Gene	Organism	Entry
`UniProtKB:Q9XDN4`	Bacterial microcompartment assembly protein PduM	pduM	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (`NCBITaxon:99287`)	REVIEWED
Role and evidence (1 reference) The single reviewed UniProtKB entry for gene pduM in Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, a taxon this record names. Identifier for the component's declared gene symbol; it is not itself evidence that the protein is part of this structure. `PMID:22343294` Sinha S et al. 2012, ‘The PduM protein is a structural component of the microcompartments involved in coenzyme B(12)-dependent 1,2-propanediol degradation by Salmonella enterica.’, J Bacteriol. ECO:0000269 experimental evidence cited by UniProt for the 'Bacterial microcompartment' localisation of Q9XDN4.

Taxonomic distribution

NCBITaxon:2 Bacteria — VARIABLE: Propanediol-utilization bacterial microcompartment loci are patchy across Bacteria and occur as one BMC type among many. [DOI:10.1038/s41467-021-24126-4]

Canonical examples

NCBITaxon:99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 — Salmonella Typhimurium LT2 is the source of the classic pdu locus and of the native Pdu metabolosomes purified, quantified, and imaged in mechanistic studies. [DOI:10.1128/JB.185.17.5086-5095.2003]

Functions

1,2-propanediol catabolic process GO:0051144 — Compartmentalizes cobalamin-dependent 1,2-propanediol dehydration and downstream propionaldehyde metabolism.
- DOI:10.1128/JB.184.5.1253-1261.2002 Havemann et al. tied Pdu polyhedral bodies to coenzyme B12-dependent 1,2-propanediol degradation in Salmonella.
propionaldehyde sequestration — Keeps the reactive propionaldehyde intermediate inside the protein shell to limit DNA and cellular damage.
- DOI:10.1128/JB.01925-07 Sampson and Bobik showed that the Pdu microcompartment protects Salmonella from DNA and cell damage caused by a reactive propanediol catabolism intermediate.

Mechanism graphs

Pdu shell and cargo assemblies converge into a metabolosome (ASSEMBLY)

Pdu shell proteins and Pdu luminal enzymes can each form early assemblies at the cell pole. Short terminal targeting sequences and PduM then link the enzyme core to BMC-domain shell proteins so the Pdu shell closes around 1,2-propanediol-catabolic cargo.

Subject	Predicate	Object	Evidence
PduCDE diol dehydratase	co-assembles with	Pdu lumen enzyme core	`DOI:10.1038/s41467-022-30608-w` Yang et al. observed cargo assemblies that form independently at cell poles during Pdu metabolosome biogenesis.
PduM structural protein	bridges	Pdu shell-cargo assembly intermediate	`DOI:10.1038/s41467-022-30608-w` Yang et al. placed PduM between the PduB N-terminal region and cargo enzymes in the biogenesis model.
Pdu lumen enzyme core	binds	Pdu BMC-T shell proteins	`DOI:10.1073/pnas.0913199107` Fan et al. established that short N-terminal extensions package enzymes into bacterial microcompartments. `DOI:10.1128/JB.05661-11` Fan and Bobik showed that PduD's N-terminal region is sufficient for targeting PduCDE to Pdu microcompartments.
Pdu BMC-H shell proteins	tiles	Pdu shell-cargo assembly intermediate	`DOI:10.1128/JB.185.17.5086-5095.2003` Purified Salmonella Pdu polyhedral organelles contained both Pdu shell proteins and 1,2-propanediol degradation enzymes.
PduN BMC-P vertex shell protein	caps	Pdu shell-cargo assembly intermediate	`DOI:10.1002/pro.2246` Wheatley et al. assigned PduN to the pentameric vertex-protein set of bacterial microcompartment shells.
Pdu shell-cargo assembly intermediate	matures into	propanediol degradation polyhedral organelle	`DOI:10.1038/s41467-022-30608-w` Yang et al. proposed a hierarchical model in which independent shell and cargo assemblies converge during native Pdu metabolosome biogenesis.

Evidence

DOI:10.1038/s41467-020-15888-4 Yang et al. used imaging and quantitative proteomics to define the composition and organization of native Salmonella Pdu metabolosomes.
DOI:10.1038/s41467-022-30608-w Yang et al. dissected convergent shell and cargo assembly pathways of the Salmonella Pdu metabolosome.
DOI:10.1128/JB.185.17.5086-5095.2003 Havemann and Bobik purified Pdu polyhedral organelles and identified shell and enzymatic components.

Curation history

2026-09-06T08:06:19Z claude · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-06T08:08:10Z claude · CURATED_PDU_METABOLOSOME — Added Pdu shell and PduCDE components, bacterial distribution, a Salmonella example, GO:0051144 function, propionaldehyde sequestration, and a convergent shell/cargo assembly graph.
2026-09-06T08:26:34Z claude · FIX_PDU_BIOGENESIS_SCOPE — Reworded the Pdu assembly graph to describe convergent shell and cargo biogenesis instead of a cargo-first-only pathway.
2026-09-08T07:39:58Z uniprot_genes · SEED_PROTEIN_EXAMPLES — #183: added 8 protein example(s) by resolving each of the component's declared gene symbols to the single reviewed UniProtKB entry for that symbol in a taxon this record names, deduplicated by accession. Symbols resolving to more than one reviewed entry were skipped rather than chosen between.

Source: data/structures/microcompartment/propanediol_degradation_polyhedral_organelle.yaml