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Protein

Oxygen-independent coproporphyrinogen III oxidase

Gene

hemN

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the heme biosynthesis. Catalyzes the anaerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen III to yield the vinyl groups in protoporphyrinogen IX. It can use NAD or NADP, but NAD is preferred.2 Publications

Catalytic activityi

Coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine.1 Publication

Cofactori

[4Fe-4S] cluster2 PublicationsNote: Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.2 Publications

Enzyme regulationi

Inhibited by EDTA.1 Publication

Pathwayi: protoporphyrin-IX biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes protoporphyrinogen-IX from coproporphyrinogen-III (AdoMet route).
Proteins known to be involved in this subpathway in this organism are:
  1. Oxygen-independent coproporphyrinogen III oxidase (hemN)
This subpathway is part of the pathway protoporphyrin-IX biosynthesis, which is itself part of Porphyrin-containing compound metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes protoporphyrinogen-IX from coproporphyrinogen-III (AdoMet route), the pathway protoporphyrin-IX biosynthesis and in Porphyrin-containing compound metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei56S-adenosyl-L-methionine 11 Publication1
Metal bindingi62Iron-sulfur (4Fe-4S-S-AdoMet)1
Metal bindingi66Iron-sulfur (4Fe-4S-S-AdoMet)1
Binding sitei68S-adenosyl-L-methionine 2; via carbonyl oxygen1 Publication1
Metal bindingi69Iron-sulfur (4Fe-4S-S-AdoMet)1
Binding sitei112S-adenosyl-L-methionine 1; via amide nitrogen and carbonyl oxygen1 Publication1
Binding sitei145S-adenosyl-L-methionine 11 Publication1
Binding sitei172S-adenosyl-L-methionine 21 Publication1
Binding sitei184S-adenosyl-L-methionine 21 Publication1
Binding sitei209S-adenosyl-L-methionine 21 Publication1

GO - Molecular functioni

  • 4 iron, 4 sulfur cluster binding Source: EcoCyc
  • coproporphyrinogen dehydrogenase activity Source: EcoCyc
  • coproporphyrinogen oxidase activity Source: InterPro
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • protoporphyrinogen IX biosynthetic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Porphyrin biosynthesis

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciEcoCyc:HEMN-MONOMER.
ECOL316407:JW3838-MONOMER.
MetaCyc:HEMN-MONOMER.
BRENDAi1.3.99.22. 2026.
UniPathwayiUPA00251; UER00323.

Names & Taxonomyi

Protein namesi
Recommended name:
Oxygen-independent coproporphyrinogen III oxidase (EC:1.3.98.31 Publication)
Short name:
CPO
Alternative name(s):
Coproporphyrinogen III dehydrogenase
Short name:
CPDH
Gene namesi
Name:hemN
Synonyms:yihJ
Ordered Locus Names:b3867, JW3838
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11836. hemN.

Subcellular locationi

  • Cytoplasm 1 Publication

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi56Y → A or L: Loss of activity. 2 Publications1
Mutagenesisi56Y → F: Decreases activity by 50%. 2 Publications1
Mutagenesisi58H → L: Results in loss of iron-sulfur cluster and activity. 1 Publication1
Mutagenesisi62C → S: Results in loss of iron-sulfur cluster and activity. 1 Publication1
Mutagenesisi66C → S: Results in loss of iron-sulfur cluster and activity. 1 Publication1
Mutagenesisi68F → L: No effect. 1 Publication1
Mutagenesisi69C → S: Results in loss of iron-sulfur cluster and activity. 1 Publication1
Mutagenesisi71C → S: No effect on iron-sulfur cluster, but results in activity loss. 1 Publication1
Mutagenesisi111G → V: Loss of activity and much less iron-sulfur cluster formed; when associated with V-113. 1 Publication1
Mutagenesisi113G → V: Loss of activity and much less iron-sulfur cluster formed; when associated with V-111. 1 Publication1
Mutagenesisi145E → A or I: Loss of activity. Iron content reduced by about 80%. 1 Publication1
Mutagenesisi310F → A or L: Loss of activity. Iron content reduced by about 50%. Can cleave up to one molecule of S-adenosyl-L-methionine (in vitro). 1 Publication1
Mutagenesisi311Q → A: Loss of activity. No change in iron content. Can cleave up to one molecule of S-adenosyl-L-methionine (in vitro). 1 Publication1
Mutagenesisi329I → A: Loss of activity. No change in iron content. Can cleave up to one molecule of S-adenosyl-L-methionine (in vitro). 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001099411 – 457Oxygen-independent coproporphyrinogen III oxidaseAdd BLAST457

Proteomic databases

PaxDbiP32131.
PRIDEiP32131.

Interactioni

Subunit structurei

Monomer.2 Publications

Protein-protein interaction databases

BioGridi4262627. 11 interactors.
DIPiDIP-9887N.
IntActiP32131. 7 interactors.
STRINGi511145.b3867.

Structurei

Secondary structure

1457
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni10 – 12Combined sources3
Beta strandi25 – 27Combined sources3
Helixi29 – 31Combined sources3
Helixi38 – 45Combined sources8
Beta strandi53 – 59Combined sources7
Beta strandi61 – 64Combined sources4
Helixi80 – 96Combined sources17
Helixi97 – 100Combined sources4
Beta strandi105 – 113Combined sources9
Helixi115 – 117Combined sources3
Helixi120 – 133Combined sources14
Beta strandi136 – 146Combined sources11
Beta strandi148 – 150Combined sources3
Helixi154 – 161Combined sources8
Beta strandi166 – 172Combined sources7
Helixi176 – 182Combined sources7
Helixi188 – 200Combined sources13
Beta strandi207 – 213Combined sources7
Helixi219 – 232Combined sources14
Beta strandi235 – 241Combined sources7
Turni246 – 248Combined sources3
Helixi250 – 254Combined sources5
Helixi257 – 259Combined sources3
Helixi263 – 279Combined sources17
Beta strandi283 – 286Combined sources4
Beta strandi289 – 291Combined sources3
Helixi296 – 303Combined sources8
Beta strandi313 – 315Combined sources3
Beta strandi320 – 325Combined sources6
Beta strandi329 – 332Combined sources4
Beta strandi335 – 339Combined sources5
Helixi343 – 353Combined sources11
Beta strandi357 – 362Combined sources6
Helixi365 – 380Combined sources16
Beta strandi381 – 384Combined sources4
Helixi385 – 391Combined sources7
Helixi396 – 399Combined sources4
Helixi401 – 412Combined sources12
Beta strandi415 – 418Combined sources4
Beta strandi420 – 425Combined sources6
Turni427 – 429Combined sources3
Helixi430 – 432Combined sources3
Helixi433 – 438Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1OLTX-ray2.07A1-457[»]
ProteinModelPortaliP32131.
SMRiP32131.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP32131.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni113 – 114S-adenosyl-L-methionine 2 binding2

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105D4P. Bacteria.
COG0635. LUCA.
HOGENOMiHOG000257214.
InParanoidiP32131.
KOiK02495.
OMAiCEIDPRH.
PhylomeDBiP32131.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
3.80.30.20. 1 hit.
InterProiIPR004558. Coprogen_oxidase_HemN.
IPR006638. Elp3/MiaB/NifB.
IPR010723. HemN_C.
IPR007197. rSAM.
IPR023404. rSAM_horseshoe.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF06969. HemN_C. 1 hit.
PF04055. Radical_SAM. 1 hit.
[Graphical view]
PIRSFiPIRSF000167. HemN. 1 hit.
SMARTiSM00729. Elp3. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00538. hemN. 1 hit.

Sequencei

Sequence statusi: Complete.

P32131-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVQQIDWDL ALIQKYNYSG PRYTSYPTAL EFSEDFGEQA FLQAVARYPE
60 70 80 90 100
RPLSLYVHIP FCHKLCYFCG CNKIVTRQQH KADQYLDALE QEIVHRAPLF
110 120 130 140 150
AGRHVSQLHW GGGTPTYLNK AQISRLMKLL RENFQFNADA EISIEVDPRE
160 170 180 190 200
IELDVLDHLR AEGFNRLSMG VQDFNKEVQR LVNREQDEEF IFALLNHARE
210 220 230 240 250
IGFTSTNIDL IYGLPKQTPE SFAFTLKRVA ELNPDRLSVF NYAHLPTIFA
260 270 280 290 300
AQRKIKDADL PSPQQKLDIL QETIAFLTQS GYQFIGMDHF ARPDDELAVA
310 320 330 340 350
QREGVLHRNF QGYTTQGDTD LLGMGVSAIS MIGDCYAQNQ KELKQYYQQV
360 370 380 390 400
DEQGNALWRG IALTRDDCIR RDVIKSLICN FRLDYAPIEK QWDLHFADYF
410 420 430 440 450
AEDLKLLAPL AKDGLVDVDE KGIQVTAKGR LLIRNICMCF DTYLRQKARM

QQFSRVI
Length:457
Mass (Da):52,729
Last modified:November 1, 1997 - v4
Checksum:i047EBB65D9B8F133
GO

Sequence cautioni

The sequence AAB03001 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti232L → V in CAA57578 (PubMed:7768836).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D16509 Genomic DNA. Translation: BAA03961.1.
X82073 Genomic DNA. Translation: CAA57578.1.
L19201 Genomic DNA. Translation: AAB03001.1. Different initiation.
U00096 Genomic DNA. Translation: AAC76864.2.
AP009048 Genomic DNA. Translation: BAE77442.1.
RefSeqiNP_418303.2. NC_000913.3.
WP_000116090.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76864; AAC76864; b3867.
BAE77442; BAE77442; BAE77442.
GeneIDi948362.
KEGGiecj:JW3838.
eco:b3867.
PATRICi32123235. VBIEscCol129921_3978.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D16509 Genomic DNA. Translation: BAA03961.1.
X82073 Genomic DNA. Translation: CAA57578.1.
L19201 Genomic DNA. Translation: AAB03001.1. Different initiation.
U00096 Genomic DNA. Translation: AAC76864.2.
AP009048 Genomic DNA. Translation: BAE77442.1.
RefSeqiNP_418303.2. NC_000913.3.
WP_000116090.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1OLTX-ray2.07A1-457[»]
ProteinModelPortaliP32131.
SMRiP32131.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262627. 11 interactors.
DIPiDIP-9887N.
IntActiP32131. 7 interactors.
STRINGi511145.b3867.

Proteomic databases

PaxDbiP32131.
PRIDEiP32131.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76864; AAC76864; b3867.
BAE77442; BAE77442; BAE77442.
GeneIDi948362.
KEGGiecj:JW3838.
eco:b3867.
PATRICi32123235. VBIEscCol129921_3978.

Organism-specific databases

EchoBASEiEB1782.
EcoGeneiEG11836. hemN.

Phylogenomic databases

eggNOGiENOG4105D4P. Bacteria.
COG0635. LUCA.
HOGENOMiHOG000257214.
InParanoidiP32131.
KOiK02495.
OMAiCEIDPRH.
PhylomeDBiP32131.

Enzyme and pathway databases

UniPathwayiUPA00251; UER00323.
BioCyciEcoCyc:HEMN-MONOMER.
ECOL316407:JW3838-MONOMER.
MetaCyc:HEMN-MONOMER.
BRENDAi1.3.99.22. 2026.

Miscellaneous databases

EvolutionaryTraceiP32131.
PROiP32131.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
3.80.30.20. 1 hit.
InterProiIPR004558. Coprogen_oxidase_HemN.
IPR006638. Elp3/MiaB/NifB.
IPR010723. HemN_C.
IPR007197. rSAM.
IPR023404. rSAM_horseshoe.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF06969. HemN_C. 1 hit.
PF04055. Radical_SAM. 1 hit.
[Graphical view]
PIRSFiPIRSF000167. HemN. 1 hit.
SMARTiSM00729. Elp3. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00538. hemN. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiHEMN_ECOLI
AccessioniPrimary (citable) accession number: P32131
Secondary accession number(s): P76772, Q2M8G4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: November 1, 1997
Last modified: November 30, 2016
This is version 146 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The structure carries two S-adenosyl-L-methionine binding sites with only one binding to iron-cluster.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.