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    PyrD Cytidine/deoxycytidylate deaminase family protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 827843, updated on 18-Sep-2024

    Summary

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    Official Symbol
    PyrD
    Official Full Name
    Cytidine/deoxycytidylate deaminase family protein
    Primary source
    TAIR:AT4G20960
    Locus tag
    AT4G20960
    See related
    Araport:AT4G20960
    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
    pyrimidine deaminase; T13K14.120; T13K14_120
    Summary
    encodes diaminohydroxyphosphoribosylaminopyrimidine deaminase catalyzing the second step in the riboflavin biosynthesis
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    Genomic context

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    See PyrD in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    3
    Sequence:
    Chromosome: 4; NC_003075.7 (11211244..11213696)

    Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene uncharacterized protein Neighboring gene basic helix-loop-helix (bHLH) DNA-binding superfamily protein Neighboring gene Eukaryotic translation initiation factor 3 subunit 7 (eIF-3)

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003075.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Evolution of vitamin B2 biosynthesis: structural and functional similarity between pyrimidine deaminases of eubacterial and plant origin. Fischer M, et al. J Biol Chem, 2004 Aug 27. PMID 15208317
    2. Proximity labeling of protein complexes and cell-type-specific organellar proteomes in Arabidopsis enabled by TurboID. Mair A, et al. Elife, 2019 Sep 19. PMID 31535972, Free PMC Article
    3. AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins. Ferro M, et al. Mol Cell Proteomics, 2010 Jun. PMID 20061580, Free PMC Article
    4. A proteomic strategy for global analysis of plant protein complexes. Aryal UK, et al. Plant Cell, 2014 Oct. PMID 25293756, Free PMC Article
    5. Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. Zybailov B, et al. PLoS One, 2008 Apr 23. PMID 18431481, Free PMC Article

    See all (6) 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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    NM_118214.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables diaminohydroxyphosphoribosylaminopyrimidine deaminase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables diaminohydroxyphosphoribosylaminopyrimidine deaminase activity IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within riboflavin biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in riboflavin biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chloroplast HDA PubMed 
    located_in chloroplast ISM
    Inferred from Sequence Model
    more info
    		  
    located_in chloroplast stroma HDA PubMed 

    General protein information

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    Preferred Names
    Cytidine/deoxycytidylate deaminase family protein
    NP_567618.1
    • Cytidine/deoxycytidylate deaminase family protein; FUNCTIONS IN: hydrolase activity, zinc ion binding, diaminohydroxyphosphoribosylaminopyrimidine deaminase activity; INVOLVED IN: riboflavin biosynthetic process; LOCATED IN: chloroplast; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: APOBEC/CMP deaminase, zinc-binding (InterPro:IPR016192), CMP/dCMP deaminase, zinc-binding (InterPro:IPR002125), Cytidine deaminase-like (InterPro:IPR016193), Riboflavin biosynthesis protein RibD (InterPro:IPR004794); BEST Arabidopsis thaliana protein match is: cytidine/deoxycytidylate deaminase family protein (TAIR:AT3G47390.2); 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).

    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_003075.7 Reference assembly

      Range
      11211244..11213696
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_118214.4 → NP_567618.1  Cytidine/deoxycytidylate deaminase family protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_567618.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8GWP5, Q8L8N0, Q9SUB7
      UniProtKB/TrEMBL
      A0A178V1S0, A0A5S9XUE5
      Conserved Domains (1) summary
      PLN02807
      Location:41 → 426
      PLN02807; diaminohydroxyphosphoribosylaminopyrimidine deaminase
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8GWP5.1

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