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    HMBS hydroxymethylbilane synthase [ Homo sapiens (human) ]

    Gene ID: 3145, updated on 22-Apr-2017
    Official Symbol
    HMBSprovided by HGNC
    Official Full Name
    hydroxymethylbilane synthaseprovided by HGNC
    Primary source
    HGNC:HGNC:4982
    See related
    Ensembl:ENSG00000256269 MIM:609806; Vega:OTTHUMG00000168295
    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]
    Orthologs
    Location:
    11q23.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 11 NC_000011.10 (119084871..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

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    • 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...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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
     
    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
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    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

    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
      5001..13673
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000190.3NP_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, OTTHUMP00000238530, ENST00000278715.7, OTTHUMT00000399188
      Conserved Domains (2) summary
      PRK00072
      Location:18344
      hemC; porphobilinogen deaminase; Reviewed
      cd13645
      Location:20299
      PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold
    2. NM_001024382.1NP_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)
      BC019323, BF210364, BQ020524, 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, OTTHUMP00000238537, ENST00000544387.5, OTTHUMT00000399195
      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, OTTHUMP00000238533, ENST00000542729.5, OTTHUMT00000399191
      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 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p7 Primary Assembly

      Range
      119084871..119093549
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005271533.3XP_005271590.1  porphobilinogen deaminase isoform X2

      Related
      ENSP00000445429.1, OTTHUMP00000238539, ENST00000543090.5, OTTHUMT00000399197
      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
    2. XM_005271532.1XP_005271589.1  porphobilinogen deaminase isoform X1

      See identical proteins and their annotated locations for XP_005271589.1

      UniProtKB/Swiss-Prot
      P08397
      Related
      ENSP00000392041.2, OTTHUMP00000238580, ENST00000442944.6, OTTHUMT00000399309
      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. 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, OTTHUMP00000238532, ENST00000537841.5, OTTHUMT00000399190
      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_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
    5. 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.p7 PATCHES

    Genomic

    1. NW_009646203.1 Reference GRCh38.p7 PATCHES

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

    Alternate CHM1_1.1

    Genomic

    1. NC_018922.2 Alternate CHM1_1.1

      Range
      118841878..118850561
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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