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HMBS hydroxymethylbilane synthase [ Homo sapiens (human) ]

Gene ID: 3145, updated on 7-Dec-2018

Summary

Official Symbol
HMBSprovided by HGNC
Official Full Name
hydroxymethylbilane synthaseprovided by HGNC
Primary source
HGNC:HGNC:4982
See related
Ensembl:ENSG00000256269 MIM:609806
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
UPS; PBGD; PORC; PBG-D
Summary
This gene encodes a member of the hydroxymethylbilane synthase superfamily. The encoded protein is the third enzyme of the heme biosynthetic pathway and catalyzes the head to tail condensation of four porphobilinogen molecules into the linear hydroxymethylbilane. Mutations in this gene are associated with the autosomal dominant disease acute intermittent porphyria. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
Expression
Biased expression in bone marrow (RPKM 55.8), colon (RPKM 5.0) and 13 other tissues See more
Orthologs

Genomic context

See HMBS in Genome Data Viewer
Location:
11q23.3
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (119084864..119093549)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118955587..118964259)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene hypoxia up-regulated 1 Neighboring gene VPS11, CORVET/HOPS core subunit Neighboring gene H2A histone family member X Neighboring gene dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 Neighboring gene uncharacterized LOC107984397

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Heme Biosynthesis, organism-specific biosystem (from WikiPathways)
    Heme Biosynthesis, organism-specific biosystemThe enzymatic process that produces heme is properly called porphyrin synthesis, as all the intermediates are tetrapyrroles that are chemically classified are porphyrins. The process is highly conser...
  • Heme biosynthesis, organism-specific biosystem (from REACTOME)
    Heme biosynthesis, organism-specific biosystemEight enzymes are involved in heme biosynthesis, four each in the mitochondria and the cytosol. The process starts in the mitochondria with the condensation of succinyl CoA (from the TCA cycle) and g...
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of porphyrins, organism-specific biosystem (from REACTOME)
    Metabolism of porphyrins, organism-specific biosystemPorphyrins are heterocyclic macrocycles, consisting of four pyrrole subunits (tetrapyrrole) linked by four methine (=CH-) bridges. The extensive conjugated porphyrin macrocycle is chromatic and the n...
  • Porphyrin and chlorophyll metabolism, organism-specific biosystem (from KEGG)
    Porphyrin and chlorophyll metabolism, organism-specific biosystem
    Porphyrin and chlorophyll metabolism
  • Porphyrin and chlorophyll metabolism, conserved biosystem (from KEGG)
    Porphyrin and chlorophyll metabolism, conserved biosystem
    Porphyrin and chlorophyll metabolism
  • heme biosynthesis, organism-specific biosystem (from BIOCYC)
    heme biosynthesis, organism-specific biosystemGeneral Background Heme (protoheme, heme b) is an iron-containing porphyrin, that belongs to the family of macrocyclic tetrapyrroles. It has a diverse range of biological functions as a prosthetic g...
  • superpathway of heme biosynthesis from glycine, conserved biosystem (from BIOCYC)
    superpathway of heme biosynthesis from glycine, conserved biosystemGeneral Background Heme (protoheme, heme b) is an iron-containing prosthetic group found in many essential proteins including cytochromes and heme-containing globins. In addition to its role in oxi...
  • tetrapyrrole biosynthesis, organism-specific biosystem (from BIOCYC)
    tetrapyrrole biosynthesis, organism-specific biosystemBackground Tetrapyrroles play a role in a variety of biological processes such as photosynthesis and respiration. They are large macrocyclic compounds derived from a common biosynthetic pathway . Te...
  • tetrapyrrole biosynthesis II (from glycine), conserved biosystem (from BIOCYC)
    tetrapyrrole biosynthesis II (from glycine), conserved biosystemTetrapyrrole compounds include four rings of the pyrrole type, generally linked together by single-atom bridges between the alpha positions of the five-membered pyrrole rings. Tetrapyrroles usually f...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
hydroxymethylbilane synthase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
hydroxymethylbilane synthase activity IDA
Inferred from Direct Assay
more info
PubMed 
hydroxymethylbilane synthase activity TAS
Traceable Author Statement
more info
 
Process Evidence Code Pubs
heme biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
heme biosynthetic process IC
Inferred by Curator
more info
PubMed 
heme biosynthetic process TAS
Traceable Author Statement
more info
 
peptidyl-pyrromethane cofactor linkage IEA
Inferred from Electronic Annotation
more info
 
protoporphyrinogen IX biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
porphobilinogen deaminase
Names
porphyria, acute; Chester type
pre-uroporphyrinogen synthase
uroporphyrinogen I synthase
uroporphyrinogen I synthetase
NP_000181.2
NP_001019553.1
NP_001245137.1
NP_001245138.1
XP_005271588.1
XP_005271589.1
XP_005271590.1
XP_011541098.1
XP_016873118.1
XP_024304228.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008093.1 RefSeqGene

    Range
    5005..13673
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1076

mRNA and Protein(s)

  1. NM_000190.4NP_000181.2  porphobilinogen deaminase isoform 1

    See identical proteins and their annotated locations for NP_000181.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AW139390, BC019323, CB128006
    Consensus CDS
    CCDS8409.1
    UniProtKB/Swiss-Prot
    P08397
    Related
    ENSP00000278715.3, ENST00000278715.7
    Conserved Domains (1) summary
    cd13645
    Location:20299
    PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold
  2. NM_001024382.2NP_001019553.1  porphobilinogen deaminase isoform 2

    See identical proteins and their annotated locations for NP_001019553.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate, in-frame exon in the 5' coding region and uses a downstream start codon, compared to variant 1. It encodes isoform 2, which has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AA724756, AP003391, BX647328, X04217
    Consensus CDS
    CCDS41726.1
    UniProtKB/Swiss-Prot
    P08397
    Related
    ENSP00000376584.1, ENST00000392841.1
    Conserved Domains (2) summary
    PRK00072
    Location:1327
    hemC; porphobilinogen deaminase; Reviewed
    cd13645
    Location:3282
    PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold
  3. NM_001258208.1NP_001245137.1  porphobilinogen deaminase isoform 3

    See identical proteins and their annotated locations for NP_001245137.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AK131072, AW139390, CB128006
    Consensus CDS
    CCDS58186.1
    UniProtKB/Swiss-Prot
    P08397
    Related
    ENSP00000438424.1, ENST00000544387.5
    Conserved Domains (2) summary
    PRK00072
    Location:18304
    hemC; porphobilinogen deaminase; Reviewed
    cd13645
    Location:20259
    PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold
  4. NM_001258209.1NP_001245138.1  porphobilinogen deaminase isoform 4

    See identical proteins and their annotated locations for NP_001245138.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice junction at the 3' end of the first exon and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (4) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform 1.
    Source sequence(s)
    AK000628, AP003392, AW139390, CB128006
    Consensus CDS
    CCDS58187.1
    UniProtKB/Swiss-Prot
    P08397
    Related
    ENSP00000443058.1, ENST00000542729.5
    Conserved Domains (2) summary
    PRK00072
    Location:1287
    hemC; porphobilinogen deaminase; Reviewed
    cd13645
    Location:3242
    PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    119084864..119093549
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024448460.1XP_024304228.1  porphobilinogen deaminase isoform X4

    Conserved Domains (1) summary
    cd13645
    Location:12241
    PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold
  2. XM_005271533.3XP_005271590.1  porphobilinogen deaminase isoform X2

    Related
    ENSP00000445429.1, ENST00000543090.5
    Conserved Domains (2) summary
    PRK00072
    Location:12326
    hemC; porphobilinogen deaminase; Reviewed
    cd13645
    Location:12281
    PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold
  3. XM_005271532.1XP_005271589.1  porphobilinogen deaminase isoform X1

    See identical proteins and their annotated locations for XP_005271589.1

    UniProtKB/Swiss-Prot
    P08397
    Conserved Domains (2) summary
    PRK00072
    Location:1327
    hemC; porphobilinogen deaminase; Reviewed
    cd13645
    Location:3282
    PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold
  4. XM_005271531.1XP_005271588.1  porphobilinogen deaminase isoform X1

    See identical proteins and their annotated locations for XP_005271588.1

    UniProtKB/Swiss-Prot
    P08397
    Related
    ENSP00000444730.1, ENST00000537841.5
    Conserved Domains (2) summary
    PRK00072
    Location:1327
    hemC; porphobilinogen deaminase; Reviewed
    cd13645
    Location:3282
    PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold
  5. XM_017017629.1XP_016873118.1  porphobilinogen deaminase isoform X1

    UniProtKB/Swiss-Prot
    P08397
    Conserved Domains (2) summary
    PRK00072
    Location:1327
    hemC; porphobilinogen deaminase; Reviewed
    cd13645
    Location:3282
    PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold
  6. XM_011542796.1XP_011541098.1  porphobilinogen deaminase isoform X3

    Conserved Domains (2) summary
    PRK00072
    Location:1289
    hemC; porphobilinogen deaminase; Reviewed
    cd13645
    Location:1244
    PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold

Reference GRCh38.p12 PATCHES

Genomic

  1. NW_009646203.1 Reference GRCh38.p12 PATCHES

    Range
    106476..106757
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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