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    HEMC hydroxymethylbilane synthase [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 830724, updated on 18-Sep-2024

    Summary

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    Official Symbol
    HEMC
    Official Full Name
    hydroxymethylbilane synthase
    Primary source
    TAIR:AT5G08280
    Locus tag
    AT5G08280
    See related
    Araport:AT5G08280
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    F8L15.10; F8L15_10; hydroxymethylbilane synthase; PORPHOBILINOGEN DEAMINASE; RUG1; RUGOSA 1
    Summary
    Encodes a protein with porphobilinogen deaminase activity. This protein is targeted to the chloroplast. Mutants spontaneously develop chlorotic leaf lesions in the absence of pathogen attack, resembling the phenotype of lesion-mimic mutants.
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    Genomic context

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    See HEMC in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    5
    Sequence:
    Chromosome: 5; NC_003076.8 (2663499..2665826, complement)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene Cytochrome P450 superfamily protein Neighboring gene serine carboxypeptidase-like 35 Neighboring gene C5orf35 Neighboring gene ncRNA Neighboring gene mRNA splicing factor, thioredoxin-like U5 snRNP Neighboring gene Succinyl-CoA ligase, alpha subunit

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003076.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Porphobilinogen deaminase is encoded by a single gene in Arabidopsis thaliana and is targeted to the chloroplasts. Lim SH, et al. Plant Mol Biol, 1994 Nov. PMID 8000000
    2. Purification and properties of porphobilinogen deaminase from Arabidopsis thaliana. Jones RM, et al. Biochem J, 1994 May 1. PMID 8192681, Free PMC Article
    3. Insights into the mechanism of pyrrole polymerization catalysed by porphobilinogen deaminase: high-resolution X-ray studies of the Arabidopsis thaliana enzyme. Roberts A, et al. Acta Crystallogr D Biol Crystallogr, 2013 Mar. PMID 23519422
    4. PORPHOBILINOGEN DEAMINASE deficiency alters vegetative and reproductive development and causes lesions in Arabidopsis. Quesada V, et al. PLoS One, 2013. PMID 23308205, Free PMC Article
    5. Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Arabidopsis thaliana. Roberts A, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2012 Dec 1. PMID 23192030, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. These results showed that both porphobilinogen deaminase (HEMC) and multiple organellar RNA editing factor (MORF) proteins are associated with AtECB2 for RNA editing in plastids.
      Title: Porphobilinogen deaminase HEMC interacts with the PPR-protein AtECB2 for chloroplast RNA editing.
    2. The interactions observed between the two pyrrole rings of the HEMC dipyrromethane cofactor and the active-site residues are highly specific and are most likely to represent the catalytically relevant binding mode.
      Title: Insights into the mechanism of pyrrole polymerization catalysed by porphobilinogen deaminase: high-resolution X-ray studies of the Arabidopsis thaliana enzyme.
    3. Porphobilinogen deaminase deficiency alters vegetative and reproductive development and causes lesions in Arabidopsis.
      Title: PORPHOBILINOGEN DEAMINASE deficiency alters vegetative and reproductive development and causes lesions in Arabidopsis.
    4. Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Arabidopsis thaliana. [porphobilinogen deaminase]
      Title: Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Arabidopsis thaliana.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_120911.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables hydroxymethylbilane synthase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables hydroxymethylbilane synthase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chlorophyll biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within chlorophyll biosynthetic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within chloroplast RNA modification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within porphyrin-containing compound biosynthetic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in protoporphyrinogen IX biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in apoplast HDA PubMed 
    located_in chloroplast HDA PubMed 
    located_in chloroplast IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chloroplast ISM
    Inferred from Sequence Model
    more info
    		  
    located_in chloroplast envelope HDA PubMed 
    located_in chloroplast stroma HDA PubMed 
    located_in plasma membrane HDA PubMed 

    General protein information

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    Preferred Names
    hydroxymethylbilane synthase
    NP_196445.1
    • hydroxymethylbilane synthase (HEMC); FUNCTIONS IN: hydroxymethylbilane synthase activity; INVOLVED IN: chlorophyll biosynthetic process, defense response to bacterium, porphyrin biosynthetic process; LOCATED IN: apoplast, chloroplast, chloroplast stroma, chloroplast envelope; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Porphobilinogen deaminase, dipyrromethane cofactor binding site (InterPro:IPR022419), Tetrapyrrole biosynthesis, hydroxymethylbilane synthase (InterPro:IPR000860), Porphobilinogen deaminase, N-terminal (InterPro:IPR022417), Porphobilinogen deaminase, C-terminal domain (InterPro:IPR022418); Has 7343 Blast hits to 7329 proteins in 2247 species: Archae - 198; Bacteria - 4150; Metazoa - 157; Fungi - 178; Plants - 78; Viruses - 0; Other Eukaryotes - 2582 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

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

    Reference assembly

    Genomic

    1. NC_003076.8 Reference assembly

      Range
      2663499..2665826 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_120911.4 → NP_196445.1  hydroxymethylbilane synthase [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_196445.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q43316, Q8LBT0
      UniProtKB/TrEMBL
      A0A178UG85, A0A5S9Y315, A0A654FZE6
      Conserved Domains (1) summary
      PLN02691
      Location:36 → 382
      PLN02691; porphobilinogen deaminase
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q43316.1

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