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Entry version 158 (17 Jun 2020)
Sequence version 1 (01 Dec 1992)
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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:4 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

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

Miscellaneous

The porphobilinogen subunits are added to the dipyrromethane group.By similarity
Present with 8480 molecules/cell in log phase SD medium.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

dipyrromethaneNote: Binds 1 dipyrromethane group covalently.

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: protoporphyrin-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.

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionTransferase
Biological processHeme biosynthesis, Porphyrin biosynthesis

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
YEAST:YDL205C-MONOMER

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-SCE-189451 Heme biosynthesis

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00251;UER00319

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:HEM3
Ordered Locus Names:YDL205C
ORF Names:D1057
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome IV

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
FungiDB:YDL205C

Saccharomyces Genome Database

More...
SGDi
S000002364 HEM3

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001430451 – 327Porphobilinogen deaminaseAdd BLAST327

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei251S-(dipyrrolylmethanemethyl)cysteineBy similarity1

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
P28789

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P28789

PRoteomics IDEntifications database

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PRIDEi
P28789

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
P28789

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

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BioGRIDi
31841, 19 interactors

STRING: functional protein association networks

More...
STRINGi
4932.YDL205C

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...
RNActi
P28789 protein

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P28789

Database of comparative protein structure models

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ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the HMBS family.Curated

Phylogenomic databases

Ensembl GeneTree

More...
GeneTreei
ENSGT00390000009083

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_019704_0_2_1

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
P28789

KEGG Orthology (KO)

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KOi
K01749

Identification of Orthologs from Complete Genome Data

More...
OMAi
LWQANHI

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
3.30.160.40, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR000860 HemC
IPR022419 Porphobilin_deaminase_cofac_BS
IPR022417 Porphobilin_deaminase_N
IPR022418 Porphobilinogen_deaminase_C
IPR036803 Porphobilinogen_deaminase_C_sf

The PANTHER Classification System

More...
PANTHERi
PTHR11557 PTHR11557, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01379 Porphobil_deam, 1 hit
PF03900 Porphobil_deamC, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF001438 4pyrrol_synth_OHMeBilane_synth, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR00151 PORPHBDMNASE

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF54782 SSF54782, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00212 hemC, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00533 PORPHOBILINOGEN_DEAM, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i1D22FF3B131ECE73
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
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

Protein sequence database of the Protein Information Resource

More...
PIRi
S25071

NCBI Reference Sequences

More...
RefSeqi
NP_010076.1, NM_001180265.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YDL205C_mRNA; YDL205C; YDL205C

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
851322

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YDL205C

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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

SMRiP28789
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi31841, 19 interactors
STRINGi4932.YDL205C

PTM databases

iPTMnetiP28789

Proteomic databases

MaxQBiP28789
PaxDbiP28789
PRIDEiP28789

Genome annotation databases

EnsemblFungiiYDL205C_mRNA; YDL205C; YDL205C
GeneIDi851322
KEGGisce:YDL205C

Organism-specific databases

EuPathDBiFungiDB:YDL205C
SGDiS000002364 HEM3

Phylogenomic databases

GeneTreeiENSGT00390000009083
HOGENOMiCLU_019704_0_2_1
InParanoidiP28789
KOiK01749
OMAiLWQANHI

Enzyme and pathway databases

UniPathwayiUPA00251;UER00319
BioCyciYEAST:YDL205C-MONOMER
ReactomeiR-SCE-189451 Heme biosynthesis

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P28789
RNActiP28789 protein

Family and domain databases

Gene3Di3.30.160.40, 1 hit
InterProiView protein in InterPro
IPR000860 HemC
IPR022419 Porphobilin_deaminase_cofac_BS
IPR022417 Porphobilin_deaminase_N
IPR022418 Porphobilinogen_deaminase_C
IPR036803 Porphobilinogen_deaminase_C_sf
PANTHERiPTHR11557 PTHR11557, 1 hit
PfamiView protein in Pfam
PF01379 Porphobil_deam, 1 hit
PF03900 Porphobil_deamC, 1 hit
PIRSFiPIRSF001438 4pyrrol_synth_OHMeBilane_synth, 1 hit
PRINTSiPR00151 PORPHBDMNASE
SUPFAMiSSF54782 SSF54782, 1 hit
TIGRFAMsiTIGR00212 hemC, 1 hit
PROSITEiView protein in PROSITE
PS00533 PORPHOBILINOGEN_DEAM, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiHEM3_YEAST
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P28789
Secondary accession number(s): D6VRE9, Q2VQW9
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 1, 1992
Last modified: June 17, 2020
This is version 158 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

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
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