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Protein

Uroporphyrinogen decarboxylase

Gene

HEM12

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

Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III.By similarity

Catalytic activityi

Uroporphyrinogen III = coproporphyrinogen + 4 CO2.

Pathwayi: protoporphyrin-IX biosynthesis

This protein is involved in step 4 of the subpathway that synthesizes coproporphyrinogen-III from 5-aminolevulinate.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Delta-aminolevulinic acid dehydratase (HEM2)
  2. Porphobilinogen deaminase (HEM3)
  3. Uroporphyrinogen-III synthase (HEM4)
  4. Uroporphyrinogen decarboxylase (HEM12)
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 coproporphyrinogen-III from 5-aminolevulinate, the pathway protoporphyrin-IX biosynthesis and in Porphyrin-containing compound metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei48 – 481SubstrateBy similarity
Binding sitei80 – 801SubstrateBy similarity
Binding sitei81 – 811SubstrateBy similarity
Sitei81 – 811Transition state stabilizerBy similarity
Binding sitei160 – 1601SubstrateBy similarity
Binding sitei215 – 2151SubstrateBy similarity
Binding sitei338 – 3381SubstrateBy similarity

GO - Molecular functioni

  • uroporphyrinogen decarboxylase activity Source: SGD

GO - Biological processi

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

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Heme biosynthesis, Porphyrin biosynthesis

Enzyme and pathway databases

BioCyciYEAST:YDR047W-MONOMER.
BRENDAi4.1.1.37. 984.
ReactomeiR-SCE-189451. Heme biosynthesis.
UniPathwayiUPA00251; UER00321.

Names & Taxonomyi

Protein namesi
Recommended name:
Uroporphyrinogen decarboxylase (EC:4.1.1.37)
Short name:
UPD
Short name:
URO-D
Gene namesi
Name:HEM12
Synonyms:HEM6, POP3
Ordered Locus Names:YDR047W
ORF Names:YD9609.03
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDR047W.
SGDiS000002454. HEM12.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi33 – 331G → D: Inactivation.
Mutagenesisi300 – 3001G → D: Inactivation.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 362362Uroporphyrinogen decarboxylasePRO_0000187577Add
BLAST

Proteomic databases

MaxQBiP32347.

Interactioni

Subunit structurei

Homodimer.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
RSP5P399402EBI-5711,EBI-16219

Protein-protein interaction databases

BioGridi32102. 28 interactions.
IntActiP32347. 3 interactions.
MINTiMINT-2732559.

Structurei

3D structure databases

ProteinModelPortaliP32347.
SMRiP32347. Positions 4-358.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni30 – 345Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000018302.
HOGENOMiHOG000253896.
InParanoidiP32347.
KOiK01599.
OMAiPEERIGW.
OrthoDBiEOG75XGWD.

Family and domain databases

HAMAPiMF_00218. URO_D.
InterProiIPR006361. Uroporphyrinogen_deCO2ase_HemE.
IPR000257. Uroporphyrinogen_deCOase.
[Graphical view]
PfamiPF01208. URO-D. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01464. hemE. 1 hit.
PROSITEiPS00906. UROD_1. 1 hit.
PS00907. UROD_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P32347-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGNFPAPKND LILRAAKGEK VERPPCWIMR QAGRYLPEYH EVKNNRDFFQ
60 70 80 90 100
TCRDAEIASE ITIQPVRRYR GLIDAAIIFS DILVIPQAMG MRVEMLEGKG
110 120 130 140 150
PHFPEPLRNP EDLQTVLDYK VDVLKELDWA FKAITMTRIK LDGEVPLFGF
160 170 180 190 200
CGGPWTLMVY MTEGGGSRLF RFAKQWINMY PELSHKLLQK ITDVAVEFLS
210 220 230 240 250
QQVVAGAQIL QVFESWGGEL SSVDFDEFSL PYLRQIAERV PKRLQELGIM
260 270 280 290 300
EQIPMIVFAK GSWYALDKLC CSGFDVVSLD WSWDPREAVK INKNRVTLQG
310 320 330 340 350
NLDPGVMYGS KEVITKKVKQ MIEAFGGGKS RYIVNFGHGT HPFMDPDVIK
360
FFLEECHRIG SK
Length:362
Mass (Da):41,349
Last modified:October 1, 1993 - v1
Checksum:iE9CB3A48E62BC277
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti59 – 591S → F in HEM12-6 and HEM12-12.
Natural varianti62 – 621T → I in HEM12-14.
Natural varianti107 – 1071L → S in HEM12-3 and HEM12-13.
Natural varianti215 – 2151S → N in HEM12-2 and HEM12-11.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X63721 Genomic DNA. Translation: CAA45253.1.
Z19089 Genomic DNA. Translation: CAA79514.1.
Z49209 Genomic DNA. Translation: CAA89078.1.
BK006938 Genomic DNA. Translation: DAA11895.1.
PIRiS23471.
RefSeqiNP_010332.3. NM_001180355.3.

Genome annotation databases

EnsemblFungiiYDR047W; YDR047W; YDR047W.
GeneIDi851617.
KEGGisce:YDR047W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X63721 Genomic DNA. Translation: CAA45253.1.
Z19089 Genomic DNA. Translation: CAA79514.1.
Z49209 Genomic DNA. Translation: CAA89078.1.
BK006938 Genomic DNA. Translation: DAA11895.1.
PIRiS23471.
RefSeqiNP_010332.3. NM_001180355.3.

3D structure databases

ProteinModelPortaliP32347.
SMRiP32347. Positions 4-358.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32102. 28 interactions.
IntActiP32347. 3 interactions.
MINTiMINT-2732559.

Proteomic databases

MaxQBiP32347.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDR047W; YDR047W; YDR047W.
GeneIDi851617.
KEGGisce:YDR047W.

Organism-specific databases

EuPathDBiFungiDB:YDR047W.
SGDiS000002454. HEM12.

Phylogenomic databases

GeneTreeiENSGT00390000018302.
HOGENOMiHOG000253896.
InParanoidiP32347.
KOiK01599.
OMAiPEERIGW.
OrthoDBiEOG75XGWD.

Enzyme and pathway databases

UniPathwayiUPA00251; UER00321.
BioCyciYEAST:YDR047W-MONOMER.
BRENDAi4.1.1.37. 984.
ReactomeiR-SCE-189451. Heme biosynthesis.

Miscellaneous databases

PROiP32347.

Family and domain databases

HAMAPiMF_00218. URO_D.
InterProiIPR006361. Uroporphyrinogen_deCO2ase_HemE.
IPR000257. Uroporphyrinogen_deCOase.
[Graphical view]
PfamiPF01208. URO-D. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01464. hemE. 1 hit.
PROSITEiPS00906. UROD_1. 1 hit.
PS00907. UROD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Uroporphyrinogen decarboxylase in Saccharomyces cerevisiae. HEM12 gene sequence and evidence for two conserved glycines essential for enzymatic activity."
    Garey J.R., Labbe-Bois R., Chelstowska A., Rytka J., Harrison L., Kushner J., Labbe P.
    Eur. J. Biochem. 205:1011-1016(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Molecular analysis of HEM6 (HEM12) in Saccharomyces cerevisiae, the gene for uroporphyrinogen decarboxylase."
    Diflumeri C., Larocque R., Keng T.
    Yeast 9:613-623(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "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.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "Identification of amino acid changes affecting yeast uroporphyrinogen decarboxylase activity by sequence analysis of hem12 mutant alleles."
    Chelstowska A., Zoadek T., Garey J.R., Kushner J., Rytka J., Labbe-Bois R.
    Biochem. J. 288:753-757(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTANTS.
  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].

Entry informationi

Entry nameiDCUP_YEAST
AccessioniPrimary (citable) accession number: P32347
Secondary accession number(s): D6VS35
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: July 6, 2016
This is version 149 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 9220 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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