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Protein

Porphobilinogen deaminase

Gene

HEM3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps.

Catalytic activityi

4 porphobilinogen + H2O = hydroxymethylbilane + 4 NH3.

Cofactori

dipyrromethaneNote: Binds 1 dipyrromethane group covalently.

Pathway:iprotoporphyrin-IX biosynthesis

This protein is involved in step 2 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.

GO - Molecular functioni

  • hydroxymethylbilane synthase activity Source: SGD

GO - Biological processi

  • heme biosynthetic process Source: SGD
  • peptidyl-pyrromethane cofactor linkage Source: InterPro
  • protoporphyrinogen IX biosynthetic process Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Heme biosynthesis, Porphyrin biosynthesis

Enzyme and pathway databases

BioCyciYEAST:YDL205C-MONOMER.
ReactomeiREACT_347076. Heme biosynthesis.
UniPathwayiUPA00251; UER00319.

Names & Taxonomyi

Protein namesi
Recommended name:
Porphobilinogen deaminase (EC:2.5.1.61)
Short name:
PBG
Alternative name(s):
Hydroxymethylbilane synthase
Short name:
HMBS
Pre-uroporphyrinogen synthase
Gene namesi
Name:HEM3
Ordered Locus Names:YDL205C
ORF Names:D1057
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome IV

Organism-specific databases

CYGDiYDL205c.
EuPathDBiFungiDB:YDL205C.
SGDiS000002364. HEM3.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 327327Porphobilinogen deaminasePRO_0000143045Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei251 – 2511S-(dipyrrolylmethanemethyl)cysteineBy similarity

Proteomic databases

MaxQBiP28789.
PaxDbiP28789.
PeptideAtlasiP28789.
PRIDEiP28789.

Interactioni

Protein-protein interaction databases

BioGridi31841. 17 interactions.
MINTiMINT-4479920.

Structurei

3D structure databases

ProteinModelPortaliP28789.
SMRiP28789. Positions 6-321.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the HMBS family.Curated

Phylogenomic databases

eggNOGiCOG0181.
GeneTreeiENSGT00390000009083.
HOGENOMiHOG000228587.
InParanoidiP28789.
KOiK01749.
OMAiFGAKNLW.
OrthoDBiEOG7S4XGP.

Family and domain databases

Gene3Di3.30.160.40. 1 hit.
InterProiIPR000860. HemC.
IPR022419. Porphobilin_deaminase_cofac_BS.
IPR022417. Porphobilin_deaminase_N.
IPR022418. Porphobilinogen_deaminase_C.
[Graphical view]
PANTHERiPTHR11557. PTHR11557. 1 hit.
PfamiPF01379. Porphobil_deam. 1 hit.
PF03900. Porphobil_deamC. 1 hit.
[Graphical view]
PIRSFiPIRSF001438. 4pyrrol_synth_OHMeBilane_synth. 1 hit.
PRINTSiPR00151. PORPHBDMNASE.
SUPFAMiSSF54782. SSF54782. 1 hit.
TIGRFAMsiTIGR00212. hemC. 1 hit.
PROSITEiPS00533. PORPHOBILINOGEN_DEAM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P28789-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGPETLHIGG RKSKLAVIQS NHVLKLIEEK YPDYDCKVFT LQTLGDQIQF
60 70 80 90 100
KPLYSFGGKA LWTKELEDHL YHDDPSKKLD LIVHSLKDMP TLLPEGFELG
110 120 130 140 150
GITKRVDPTD CLVMPFYSAY KSLDDLPDGG IVGTSSVRRS AQLKRKYPHL
160 170 180 190 200
KFESVRGNIQ TRLQKLDDPK SPYQCIILAS AGLMRMGLEN RITQRFHSDT
210 220 230 240 250
MYHAVGQGAL GIEIRKGDTK MMKILDEICD LNATICCLSE RALMRTLEGG
260 270 280 290 300
CSVPIGVESK YNEETKKLLL KAIVVDVEGT EAVEDEIEML IENVKEDSMA
310 320
CGKILAERMI ADGAKKILDE INLDRIK
Length:327
Mass (Da):36,675
Last modified:December 1, 1992 - v1
Checksum:i1D22FF3B131ECE73
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z11745 Genomic DNA. Translation: CAA77804.1.
X99000 Genomic DNA. Translation: CAA67486.1.
Z74253 Genomic DNA. Translation: CAA98783.1.
AY899249 mRNA. Translation: AAX83934.1.
BK006938 Genomic DNA. Translation: DAA11659.1.
PIRiS25071.
RefSeqiNP_010076.1. NM_001180265.1.

Genome annotation databases

EnsemblFungiiYDL205C; YDL205C; YDL205C.
GeneIDi851322.
KEGGisce:YDL205C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z11745 Genomic DNA. Translation: CAA77804.1.
X99000 Genomic DNA. Translation: CAA67486.1.
Z74253 Genomic DNA. Translation: CAA98783.1.
AY899249 mRNA. Translation: AAX83934.1.
BK006938 Genomic DNA. Translation: DAA11659.1.
PIRiS25071.
RefSeqiNP_010076.1. NM_001180265.1.

3D structure databases

ProteinModelPortaliP28789.
SMRiP28789. Positions 6-321.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31841. 17 interactions.
MINTiMINT-4479920.

Proteomic databases

MaxQBiP28789.
PaxDbiP28789.
PeptideAtlasiP28789.
PRIDEiP28789.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL205C; YDL205C; YDL205C.
GeneIDi851322.
KEGGisce:YDL205C.

Organism-specific databases

CYGDiYDL205c.
EuPathDBiFungiDB:YDL205C.
SGDiS000002364. HEM3.

Phylogenomic databases

eggNOGiCOG0181.
GeneTreeiENSGT00390000009083.
HOGENOMiHOG000228587.
InParanoidiP28789.
KOiK01749.
OMAiFGAKNLW.
OrthoDBiEOG7S4XGP.

Enzyme and pathway databases

UniPathwayiUPA00251; UER00319.
BioCyciYEAST:YDL205C-MONOMER.
ReactomeiREACT_347076. Heme biosynthesis.

Miscellaneous databases

NextBioi968366.
PROiP28789.

Family and domain databases

Gene3Di3.30.160.40. 1 hit.
InterProiIPR000860. HemC.
IPR022419. Porphobilin_deaminase_cofac_BS.
IPR022417. Porphobilin_deaminase_N.
IPR022418. Porphobilinogen_deaminase_C.
[Graphical view]
PANTHERiPTHR11557. PTHR11557. 1 hit.
PfamiPF01379. Porphobil_deam. 1 hit.
PF03900. Porphobil_deamC. 1 hit.
[Graphical view]
PIRSFiPIRSF001438. 4pyrrol_synth_OHMeBilane_synth. 1 hit.
PRINTSiPR00151. PORPHBDMNASE.
SUPFAMiSSF54782. SSF54782. 1 hit.
TIGRFAMsiTIGR00212. hemC. 1 hit.
PROSITEiPS00533. PORPHOBILINOGEN_DEAM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Structure and regulation of yeast HEM3, the gene for porphobilinogen deaminase."
    Keng T., Richard C., Larocque R.
    Mol. Gen. Genet. 234:233-243(1992) [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. "Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE."
    Zhang Z., Dietrich F.S.
    Nucleic Acids Res. 33:2838-2851(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-97.
    Strain: ATCC 208353 / W303-1A.
  5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  6. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiHEM3_YEAST
AccessioniPrimary (citable) accession number: P28789
Secondary accession number(s): D6VRE9, Q2VQW9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 1, 1992
Last modified: July 22, 2015
This is version 126 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

The porphobilinogen subunits are added to the dipyrromethane group.By similarity
Present with 8480 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

External Data

Dasty 3

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 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.