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    HDS 4-hydroxy-3-methylbut-2-enyl diphosphate synthase [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 836181, updated on 18-Sep-2024

    Summary

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    Official Symbol
    HDS
    Official Full Name
    4-hydroxy-3-methylbut-2-enyl diphosphate synthase
    Primary source
    TAIR:AT5G60600
    Locus tag
    AT5G60600
    See related
    Araport:AT5G60600
    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
    4-hydroxy-3-methylbut-2-enyl diphosphate synthase; CHLOROPLAST BIOGENESIS 4; CLB4; CONSTITUTIVE SUBTILISIN 3; CSB3; GCPE; ISPG; MUP24.15; MUP24_15
    Summary
    Encodes a chloroplast-localized hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase (HDS), catalyzes the formation of HMBPP from 2-C-methyl-D-erythrytol 2,4-cyclodiphosphate (MEcPP). The HDS enzyme controls the penultimate steps of the biosynthesis of IPP and dimethylallyl diphosphate (DMAPP) via the MEP pathway and may serve as a metabolic control point for SA-mediated disease resistance. In the light, the electrons required for the reaction catalyzed by HDS are directly provided by the electron flow from photosynthesis via ferredoxin. In the dark however, the enzyme requires an electron shuttle: ferredoxin-NADP<sup>+</sup> reductase.
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    Genomic context

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    See HDS in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    19
    Sequence:
    Chromosome: 5; NC_003076.8 (24358885..24363485)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene RING/U-box superfamily protein Neighboring gene DHBP synthase RibB-like alpha/beta domain-containing protein Neighboring gene F-box/RNI-like superfamily protein Neighboring gene Defensin-like (DEFL) family protein Neighboring gene glycerol-3-phosphate acyltransferase 9 Neighboring gene uncharacterized protein

    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. Uncovering the functional residues of Arabidopsis isoprenoid biosynthesis enzyme HDS. Wang JZ, et al. Proc Natl Acad Sci U S A, 2020 Jan 7. PMID 31879352, Free PMC Article
    2. The Arabidopsis csb3 mutant reveals a regulatory link between salicylic acid-mediated disease resistance and the methyl-erythritol 4-phosphate pathway. Gil MJ, et al. Plant J, 2005 Oct. PMID 16167903
    3. Isoprenoid biosynthesis in chloroplasts via the methylerythritol phosphate pathway: the (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase (GcpE) from Arabidopsis thaliana is a [4Fe-4S] protein. Seemann M, et al. J Biol Inorg Chem, 2005 Mar. PMID 15650872
    4. Functional analysis of the Arabidopsis thaliana GCPE protein involved in plastid isoprenoid biosynthesis. Querol J, et al. FEBS Lett, 2002 Mar 13. PMID 11943178
    5. The homeodomain-leucine zipper ATHB23, a phytochrome B-interacting protein, is important for phytochrome B-mediated red light signaling. Choi H, et al. Physiol Plant, 2014 Feb. PMID 23964902

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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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    Markers

    NM_001125995.2
    NM_001345428.1
    NM_125453.6
    NM_180902.5

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables 4 iron, 4 sulfur cluster binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity (ferredoxin) IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity (ferredoxin) IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity (ferredoxin) IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    enables iron ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within response to bacterium IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within systemic acquired resistance, salicylic acid mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in terpenoid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chloroplast HDA PubMed 
    located_in chloroplast IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chloroplast envelope HDA PubMed 
    located_in chloroplast stroma HDA PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  
    located_in plastid HDA PubMed 

    General protein information

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    Preferred Names
    4-hydroxy-3-methylbut-2-enyl diphosphate synthase
    NP_001119467.1
    • 4-hydroxy-3-methylbut-2-enyl diphosphate synthase (HDS); FUNCTIONS IN: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity, 4 iron, 4 sulfur cluster binding; INVOLVED IN: response to light stimulus, isoprenoid biosynthetic process, isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway, response to bacterium, systemic acquired resistance, salicylic acid mediated signaling pathway; LOCATED IN: chloroplast; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Dihydropteroate synthase-like (InterPro:IPR011005), 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, atypical (InterPro:IPR017178), 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial-type (InterPro:IPR004588); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).
    NP_200868.2
    • 4-hydroxy-3-methylbut-2-enyl diphosphate synthase (HDS); FUNCTIONS IN: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity, 4 iron, 4 sulfur cluster binding; INVOLVED IN: response to light stimulus, isoprenoid biosynthetic process, isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway, response to bacterium, systemic acquired resistance, salicylic acid mediated signaling pathway; LOCATED IN: chloroplast, chloroplast envelope; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Dihydropteroate synthase-like (InterPro:IPR011005), 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, atypical (InterPro:IPR017178), 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial-type (InterPro:IPR004588); Has 12643 Blast hits to 7322 proteins in 2058 species: Archae - 0; Bacteria - 8079; Metazoa - 2; Fungi - 2; Plants - 72; Viruses - 0; Other Eukaryotes - 4488 (source: NCBI BLink).
    NP_851233.1
    • 4-hydroxy-3-methylbut-2-enyl diphosphate synthase (HDS); FUNCTIONS IN: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity, 4 iron, 4 sulfur cluster binding; INVOLVED IN: response to light stimulus, isoprenoid biosynthetic process, isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway, response to bacterium, systemic acquired resistance, salicylic acid mediated signaling pathway; LOCATED IN: chloroplast stroma, chloroplast, chloroplast envelope; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Dihydropteroate synthase-like (InterPro:IPR011005), 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, atypical (InterPro:IPR017178), 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial-type (InterPro:IPR004588); Has 12699 Blast hits to 7350 proteins in 2074 species: Archae - 0; Bacteria - 8133; Metazoa - 2; Fungi - 2; Plants - 72; Viruses - 0; Other Eukaryotes - 4490 (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
      24358885..24363485
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001345427.1 → NP_001332136.1  4-hydroxy-3-methylbut-2-enyl diphosphate synthase [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9YFV0, B3H725

    2. NM_001125995.2 → NP_001119467.1  4-hydroxy-3-methylbut-2-enyl diphosphate synthase [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001119467.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9YFV0, B3H725
      Conserved Domains (3) summary
      PLN02925
      Location:1 → 717
      PLN02925; 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
      pfam04551
      Location:87 → 359
      GcpE; GcpE protein
      cl19500
      Location:626 → 669
      GcpE; GcpE protein

    3. NM_180902.5 → NP_851233.1  4-hydroxy-3-methylbut-2-enyl diphosphate synthase [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_851233.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      F4K0E8, Q8GZR7, Q8LPQ4, Q8RXG8, Q9FF59
      UniProtKB/TrEMBL
      A0A178UN53, A0A5S9YFV0
      Conserved Domains (1) summary
      PLN02925
      Location:1 → 740
      PLN02925; 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase

    4. NM_001345428.1 → NP_001332137.1  4-hydroxy-3-methylbut-2-enyl diphosphate synthase [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9YFV0, B3H725

    5. NM_125453.6 → NP_200868.2  4-hydroxy-3-methylbut-2-enyl diphosphate synthase [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_200868.2

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9YFV0
      Conserved Domains (3) summary
      PLN02925
      Location:1 → 739
      PLN02925; 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
      pfam04551
      Location:87 → 359
      GcpE; GcpE protein
      cl19500
      Location:625 → 728
      GcpE; GcpE protein
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    F4K0E8.1

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