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Protein

Oxygen-dependent coproporphyrinogen-III oxidase

Gene

HEM13

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the heme biosynthesis. Catalyzes the aerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen-III to yield the vinyl groups in protoporphyrinogen-IX (By similarity).By similarity

Catalytic activityi

Coproporphyrinogen-III + O2 + 2 H+ = protoporphyrinogen-IX + 2 CO2 + 2 H2O.

Pathwayi: protoporphyrin-IX biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes protoporphyrinogen-IX from coproporphyrinogen-III (O2 route).
Proteins known to be involved in this subpathway in this organism are:
  1. Oxygen-dependent coproporphyrinogen-III oxidase (HEM13)
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 (O2 route), the pathway protoporphyrin-IX biosynthesis and in Porphyrin-containing compound metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei117SubstrateBy similarity1
Active sitei131Proton donorBy similarity1
Sitei201Important for dimerizationBy similarity1

GO - Molecular functioni

  • coproporphyrinogen oxidase activity Source: SGD
  • protein homodimerization activity Source: UniProtKB

GO - Biological processi

  • heme biosynthetic process Source: SGD
  • protoporphyrinogen IX biosynthetic process Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Heme biosynthesis, Porphyrin biosynthesis

Enzyme and pathway databases

BioCyciYEAST:YDR044W-MONOMER.
ReactomeiR-SCE-189451. Heme biosynthesis.
UniPathwayiUPA00251; UER00322.

Names & Taxonomyi

Protein namesi
Recommended name:
Oxygen-dependent coproporphyrinogen-III oxidase (EC:1.3.3.3)
Short name:
COX
Short name:
Coprogen oxidase
Short name:
Coproporphyrinogenase
Gene namesi
Name:HEM13
Ordered Locus Names:YDR044W
ORF Names:YD5112.02
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDR044W.
SGDiS000002451. HEM13.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001098781 – 328Oxygen-dependent coproporphyrinogen-III oxidaseAdd BLAST328

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi193Interchain1 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

MaxQBiP11353.
PRIDEiP11353.

PTM databases

iPTMnetiP11353.

Interactioni

Subunit structurei

Homodimer.1 Publication

GO - Molecular functioni

Protein-protein interaction databases

BioGridi32099. 49 interactors.
DIPiDIP-1614N.
IntActiP11353. 10 interactors.
MINTiMINT-403879.

Structurei

Secondary structure

1328
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi7 – 9Combined sources3
Helixi12 – 32Combined sources21
Beta strandi35 – 37Combined sources3
Beta strandi40 – 45Combined sources6
Helixi47 – 49Combined sources3
Beta strandi51 – 53Combined sources3
Beta strandi55 – 60Combined sources6
Beta strandi62 – 78Combined sources17
Helixi80 – 84Combined sources5
Helixi87 – 89Combined sources3
Beta strandi99 – 102Combined sources4
Beta strandi109 – 124Combined sources16
Beta strandi129 – 140Combined sources12
Beta strandi144 – 158Combined sources15
Helixi164 – 179Combined sources16
Helixi185 – 189Combined sources5
Helixi193 – 200Combined sources8
Beta strandi204 – 207Combined sources4
Beta strandi209 – 216Combined sources8
Helixi221 – 232Combined sources12
Helixi235 – 244Combined sources10
Turni245 – 248Combined sources4
Helixi253 – 263Combined sources11
Helixi265 – 269Combined sources5
Helixi275 – 282Combined sources8
Helixi288 – 291Combined sources4
Helixi292 – 294Combined sources3
Beta strandi297 – 300Combined sources4
Helixi312 – 321Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TK1X-ray1.90A6-265[»]
1TKLX-ray2.00A/B3-328[»]
1TLBX-ray2.40A/D/Q/S/U/W3-328[»]
1TXNX-ray1.70A/B1-328[»]
ProteinModelPortaliP11353.
SMRiP11353.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP11353.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni57 – 66Important for dimerizationBy similarity10
Regioni133 – 135Substrate bindingBy similarity3
Regioni266 – 302Important for dimerizationBy similarityAdd BLAST37
Regioni285 – 290Substrate bindingBy similarity6

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000017311.
HOGENOMiHOG000262768.
InParanoidiP11353.
KOiK00228.
OMAiIDLTPHY.
OrthoDBiEOG092C2BWE.

Family and domain databases

Gene3Di3.40.1500.10. 1 hit.
InterProiIPR001260. Coprogen_oxidase_aer.
IPR018375. Coprogen_oxidase_CS.
[Graphical view]
PANTHERiPTHR10755. PTHR10755. 1 hit.
PfamiPF01218. Coprogen_oxidas. 1 hit.
[Graphical view]
PIRSFiPIRSF000166. Coproporphyri_ox. 1 hit.
PRINTSiPR00073. COPRGNOXDASE.
SUPFAMiSSF102886. SSF102886. 1 hit.
PROSITEiPS01021. COPROGEN_OXIDASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P11353-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPAPQDPRNL PIRQQMEALI RRKQAEITQG LESIDTVKFH ADTWTRGNDG
60 70 80 90 100
GGGTSMVIQD GTTFEKGGVN VSVVYGQLSP AAVSAMKADH KNLRLPEDPK
110 120 130 140 150
TGLPVTDGVK FFACGLSMVI HPVNPHAPTT HLNYRYFETW NQDGTPQTWW
160 170 180 190 200
FGGGADLTPS YLYEEDGQLF HQLHKDALDK HDTALYPRFK KWCDEYFYIT
210 220 230 240 250
HRKETRGIGG IFFDDYDERD PQEILKMVED CFDAFLPSYL TIVKRRKDMP
260 270 280 290 300
YTKEEQQWQA IRRGRYVEFN LIYDRGTQFG LRTPGSRVES ILMSLPEHAS
310 320
WLYNHHPAPG SREAKLLEVT TKPREWVK
Length:328
Mass (Da):37,712
Last modified:October 1, 1996 - v2
Checksum:i9C166F03BD0B0B4C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti226K → N in AAA34529 (PubMed:2838478).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03873 Genomic DNA. Translation: AAA34529.1.
Z49812 Genomic DNA. Translation: CAA89966.1.
AY557656 Genomic DNA. Translation: AAS55982.1.
BK006938 Genomic DNA. Translation: DAA11892.1.
PIRiS55079. DEBYCH.
RefSeqiNP_010329.1. NM_001180352.1.

Genome annotation databases

EnsemblFungiiYDR044W; YDR044W; YDR044W.
GeneIDi851614.
KEGGisce:YDR044W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03873 Genomic DNA. Translation: AAA34529.1.
Z49812 Genomic DNA. Translation: CAA89966.1.
AY557656 Genomic DNA. Translation: AAS55982.1.
BK006938 Genomic DNA. Translation: DAA11892.1.
PIRiS55079. DEBYCH.
RefSeqiNP_010329.1. NM_001180352.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TK1X-ray1.90A6-265[»]
1TKLX-ray2.00A/B3-328[»]
1TLBX-ray2.40A/D/Q/S/U/W3-328[»]
1TXNX-ray1.70A/B1-328[»]
ProteinModelPortaliP11353.
SMRiP11353.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32099. 49 interactors.
DIPiDIP-1614N.
IntActiP11353. 10 interactors.
MINTiMINT-403879.

PTM databases

iPTMnetiP11353.

Proteomic databases

MaxQBiP11353.
PRIDEiP11353.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDR044W; YDR044W; YDR044W.
GeneIDi851614.
KEGGisce:YDR044W.

Organism-specific databases

EuPathDBiFungiDB:YDR044W.
SGDiS000002451. HEM13.

Phylogenomic databases

GeneTreeiENSGT00390000017311.
HOGENOMiHOG000262768.
InParanoidiP11353.
KOiK00228.
OMAiIDLTPHY.
OrthoDBiEOG092C2BWE.

Enzyme and pathway databases

UniPathwayiUPA00251; UER00322.
BioCyciYEAST:YDR044W-MONOMER.
ReactomeiR-SCE-189451. Heme biosynthesis.

Miscellaneous databases

EvolutionaryTraceiP11353.
PROiP11353.

Family and domain databases

Gene3Di3.40.1500.10. 1 hit.
InterProiIPR001260. Coprogen_oxidase_aer.
IPR018375. Coprogen_oxidase_CS.
[Graphical view]
PANTHERiPTHR10755. PTHR10755. 1 hit.
PfamiPF01218. Coprogen_oxidas. 1 hit.
[Graphical view]
PIRSFiPIRSF000166. Coproporphyri_ox. 1 hit.
PRINTSiPR00073. COPRGNOXDASE.
SUPFAMiSSF102886. SSF102886. 1 hit.
PROSITEiPS01021. COPROGEN_OXIDASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiHEM6_YEAST
AccessioniPrimary (citable) accession number: P11353
Secondary accession number(s): D6VS32
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: October 1, 1996
Last modified: November 2, 2016
This is version 159 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 22000 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

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

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

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.