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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei117 – 1171SubstrateBy similarity
Active sitei131 – 1311Proton donorBy similarity
Sitei201 – 2011Important for dimerizationBy similarity

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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 328328Oxygen-dependent coproporphyrinogen-III oxidasePRO_0000109878Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi193 – 193Interchain1 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

MaxQBiP11353.
PeptideAtlasiP11353.

PTM databases

iPTMnetiP11353.

Interactioni

Subunit structurei

Homodimer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
ECM10P399872EBI-8257,EBI-22339
PIL1P532522EBI-8257,EBI-23225
SSA3P094352EBI-8257,EBI-8611

GO - Molecular functioni

Protein-protein interaction databases

BioGridi32099. 47 interactions.
DIPiDIP-1614N.
IntActiP11353. 10 interactions.
MINTiMINT-403879.

Structurei

Secondary structure

1
328
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi7 – 93Combined sources
Helixi12 – 3221Combined sources
Beta strandi35 – 373Combined sources
Beta strandi40 – 456Combined sources
Helixi47 – 493Combined sources
Beta strandi51 – 533Combined sources
Beta strandi55 – 606Combined sources
Beta strandi62 – 7817Combined sources
Helixi80 – 845Combined sources
Helixi87 – 893Combined sources
Beta strandi99 – 1024Combined sources
Beta strandi109 – 12416Combined sources
Beta strandi129 – 14012Combined sources
Beta strandi144 – 15815Combined sources
Helixi164 – 17916Combined sources
Helixi185 – 1895Combined sources
Helixi193 – 2008Combined sources
Beta strandi204 – 2074Combined sources
Beta strandi209 – 2168Combined sources
Helixi221 – 23212Combined sources
Helixi235 – 24410Combined sources
Turni245 – 2484Combined sources
Helixi253 – 26311Combined sources
Helixi265 – 2695Combined sources
Helixi275 – 2828Combined sources
Helixi288 – 2914Combined sources
Helixi292 – 2943Combined sources
Beta strandi297 – 3004Combined sources
Helixi312 – 32110Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 3-328.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP11353.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni57 – 6610Important for dimerizationBy similarity
Regioni133 – 1353Substrate bindingBy similarity
Regioni266 – 30237Important for dimerizationBy similarityAdd
BLAST
Regioni285 – 2906Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000017311.
HOGENOMiHOG000262768.
InParanoidiP11353.
KOiK00228.
OMAiQRPEAKG.
OrthoDBiEOG73Z33M.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti226 – 2261K → N in AAA34529 (PubMed:2838478).Curated

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
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. Positions 3-328.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32099. 47 interactions.
DIPiDIP-1614N.
IntActiP11353. 10 interactions.
MINTiMINT-403879.

PTM databases

iPTMnetiP11353.

Proteomic databases

MaxQBiP11353.
PeptideAtlasiP11353.

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.
OMAiQRPEAKG.
OrthoDBiEOG73Z33M.

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...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation, sequence, and regulation by oxygen of the yeast HEM13 gene coding for coproporphyrinogen oxidase."
    Zagorec M., Buhler J.-M., Treich I., Keng T., Guarente L., Labbe-Bois R.
    J. Biol. Chem. 263:9718-9724(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
    , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
    Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. "Purification and properties of coproporphyrinogen oxidase from the yeast Saccharomyces cerevisiae."
    Camadro J.-M., Chambon H., Jolles J., Labbe P.
    Eur. J. Biochem. 156:579-587(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: PARTIAL PROTEIN SEQUENCE, CHARACTERIZATION.
  6. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  8. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "Crystal structure of the oxygen-dependant coproporphyrinogen oxidase (Hem13p) of Saccharomyces cerevisiae."
    Phillips J.D., Whitby F.G., Warby C.A., Labbe P., Yang C., Pflugrath J.W., Ferrara J.D., Robinson H., Kushner J.P., Hill C.P.
    J. Biol. Chem. 279:38960-38968(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS), SUBUNIT, DISULFIDE BOND.

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: June 8, 2016
This is version 155 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.