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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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