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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei56 – 561S-adenosyl-L-methionine 11 Publication
Metal bindingi62 – 621Iron-sulfur (4Fe-4S-S-AdoMet)
Metal bindingi66 – 661Iron-sulfur (4Fe-4S-S-AdoMet)
Binding sitei68 – 681S-adenosyl-L-methionine 2; via carbonyl oxygen1 Publication
Metal bindingi69 – 691Iron-sulfur (4Fe-4S-S-AdoMet)
Binding sitei112 – 1121S-adenosyl-L-methionine 1; via amide nitrogen and carbonyl oxygen1 Publication
Binding sitei145 – 1451S-adenosyl-L-methionine 11 Publication
Binding sitei172 – 1721S-adenosyl-L-methionine 21 Publication
Binding sitei184 – 1841S-adenosyl-L-methionine 21 Publication
Binding sitei209 – 2091S-adenosyl-L-methionine 21 Publication

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:1.3.99.22)
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi56 – 561Y → A or L: Loss of activity. 2 Publications
Mutagenesisi56 – 561Y → F: Decreases activity by 50%. 2 Publications
Mutagenesisi58 – 581H → L: Results in loss of iron-sulfur cluster and activity. 1 Publication
Mutagenesisi62 – 621C → S: Results in loss of iron-sulfur cluster and activity. 1 Publication
Mutagenesisi66 – 661C → S: Results in loss of iron-sulfur cluster and activity. 1 Publication
Mutagenesisi68 – 681F → L: No effect. 1 Publication
Mutagenesisi69 – 691C → S: Results in loss of iron-sulfur cluster and activity. 1 Publication
Mutagenesisi71 – 711C → S: No effect on iron-sulfur cluster, but results in activity loss. 1 Publication
Mutagenesisi111 – 1111G → V: Loss of activity and much less iron-sulfur cluster formed; when associated with V-113. 1 Publication
Mutagenesisi113 – 1131G → V: Loss of activity and much less iron-sulfur cluster formed; when associated with V-111. 1 Publication
Mutagenesisi145 – 1451E → A or I: Loss of activity. Iron content reduced by about 80%. 1 Publication
Mutagenesisi310 – 3101F → 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 Publication
Mutagenesisi311 – 3111Q → A: Loss of activity. No change in iron content. Can cleave up to one molecule of S-adenosyl-L-methionine (in vitro). 1 Publication
Mutagenesisi329 – 3291I → A: Loss of activity. No change in iron content. Can cleave up to one molecule of S-adenosyl-L-methionine (in vitro). 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 457457Oxygen-independent coproporphyrinogen-III oxidasePRO_0000109941Add
BLAST

Proteomic databases

PaxDbiP32131.
PRIDEiP32131.

Interactioni

Subunit structurei

Monomer.2 Publications

Protein-protein interaction databases

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

Structurei

Secondary structure

1
457
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni10 – 123Combined sources
Beta strandi25 – 273Combined sources
Helixi29 – 313Combined sources
Helixi38 – 458Combined sources
Beta strandi53 – 597Combined sources
Beta strandi61 – 644Combined sources
Helixi80 – 9617Combined sources
Helixi97 – 1004Combined sources
Beta strandi105 – 1139Combined sources
Helixi115 – 1173Combined sources
Helixi120 – 13314Combined sources
Beta strandi136 – 14611Combined sources
Beta strandi148 – 1503Combined sources
Helixi154 – 1618Combined sources
Beta strandi166 – 1727Combined sources
Helixi176 – 1827Combined sources
Helixi188 – 20013Combined sources
Beta strandi207 – 2137Combined sources
Helixi219 – 23214Combined sources
Beta strandi235 – 2417Combined sources
Turni246 – 2483Combined sources
Helixi250 – 2545Combined sources
Helixi257 – 2593Combined sources
Helixi263 – 27917Combined sources
Beta strandi283 – 2864Combined sources
Beta strandi289 – 2913Combined sources
Helixi296 – 3038Combined sources
Beta strandi313 – 3153Combined sources
Beta strandi320 – 3256Combined sources
Beta strandi329 – 3324Combined sources
Beta strandi335 – 3395Combined sources
Helixi343 – 35311Combined sources
Beta strandi357 – 3626Combined sources
Helixi365 – 38016Combined sources
Beta strandi381 – 3844Combined sources
Helixi385 – 3917Combined sources
Helixi396 – 3994Combined sources
Helixi401 – 41212Combined sources
Beta strandi415 – 4184Combined sources
Beta strandi420 – 4256Combined sources
Turni427 – 4293Combined sources
Helixi430 – 4323Combined sources
Helixi433 – 4386Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1OLTX-ray2.07A1-457[»]
ProteinModelPortaliP32131.
SMRiP32131. Positions 4-444.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP32131.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni113 – 1142S-adenosyl-L-methionine 2 binding

Sequence similaritiesi

Phylogenomic databases

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

Family and domain databases

Gene3Di3.80.30.20. 1 hit.
InterProiIPR004558. Coprogen_oxidase_HemN.
IPR006638. Elp3/MiaB/NifB.
IPR010723. HemN_C.
IPR007197. rSAM.
IPR023404. rSAM_horseshoe.
[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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti232 – 2321L → V in CAA57578 (PubMed:7768836).Curated

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
EntryMethodResolution (Å)ChainPositionsPDBsum
1OLTX-ray2.07A1-457[»]
ProteinModelPortaliP32131.
SMRiP32131. Positions 4-444.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262627. 11 interactions.
DIPiDIP-9887N.
IntActiP32131. 7 interactions.
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

Gene3Di3.80.30.20. 1 hit.
InterProiIPR004558. Coprogen_oxidase_HemN.
IPR006638. Elp3/MiaB/NifB.
IPR010723. HemN_C.
IPR007197. rSAM.
IPR023404. rSAM_horseshoe.
[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: September 7, 2016
This is version 143 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.