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PYD1 pyrimidine 1 [ Arabidopsis thaliana (thale cress) ]

Gene ID: 821049, updated on 18-Sep-2024

Summary

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Official Symbol
PYD1
Official Full Name
pyrimidine 1
Primary source
TAIR:AT3G17810
Locus tag
AT3G17810
See related
Araport:AT3G17810
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 1
Summary
Encodes a protein predicted to have dihydropyrimidine dehydrogenase activity. Its activity has not been demonstrated in vivo, but, it is required for efficient uracil catabolism in Arabidopsis. It localizes to the plastid.
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Genomic context

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See PYD1 in Genome Data Viewer
Location:
chromosome: 3
Exon count:
7
Sequence:
Chromosome: 3; NC_003074.8 (6093990..6096688)

Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene purple acid phosphatase 17 Neighboring gene alanine-tRNA ligase, putative (DUF760) Neighboring gene ncRNA Neighboring gene glutamine synthetase 1.3 Neighboring gene Molecular chaperone Hsp40/DnaJ family protein

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003074.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. A functional analysis of the pyrimidine catabolic pathway in Arabidopsis. Zrenner R, et al. New Phytol, 2009. PMID 19413687, Free PMC Article
  2. Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA. Gao S, et al. Nucleic Acids Res, 2023 Aug 11. PMID 37334828, 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. Advanced proteomic analyses yield a deep catalog of ubiquitylation targets in Arabidopsis. Kim DY, et al. Plant Cell, 2013 May. PMID 23667124, Free PMC Article
  5. A proteomic strategy for global analysis of plant protein complexes. Aryal UK, et al. Plant Cell, 2014 Oct. PMID 25293756, Free PMC Article

See all (8) 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_112662.4

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables dihydropyrimidine dehydrogenase (NADP+) activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables thymine dehydrogenase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in beta-alanine biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within cellular response to nitrogen levels IEP
Inferred from Expression Pattern
more info
 PubMed 
acts_upstream_of_or_within uracil catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in chloroplast HDA PubMed 
located_in chloroplast stroma HDA PubMed 
located_in plasma membrane ISM
Inferred from Sequence Model
more info
  
located_in plastid IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
pyrimidine 1
NP_188408.1
  • pyrimidine 1 (PYD1); FUNCTIONS IN: oxidoreductase activity, acting on the CH-CH group of donors, dihydropyrimidine dehydrogenase (NADP+) activity; INVOLVED IN: 'de novo' pyrimidine base biosynthetic process, uracil catabolic process, cellular response to nitrogen levels; LOCATED IN: chloroplast, plastid; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Aldolase-type TIM barrel (InterPro:IPR013785), Dihydroorotate dehydrogenase, class 1/ 2 (InterPro:IPR012135), Dihydroorotate dehydrogenase, class 1, core (InterPro:IPR005720); Has 5953 Blast hits to 5953 proteins in 1914 species: Archae - 176; Bacteria - 4342; Metazoa - 263; Fungi - 99; Plants - 89; Viruses - 0; Other Eukaryotes - 984 (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_003074.8 Reference assembly

    Range
    6093990..6096688
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_112662.4 → NP_188408.1  pyrimidine 1 [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_188408.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q9LVI9
    UniProtKB/TrEMBL
    A0A178VD08, A0A5S9XD53
    Conserved Domains (1) summary
    PLN02495
    Location:44 → 426
    PLN02495; oxidoreductase, acting on the CH-CH group of donors
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9LVI9.1

Gene LinkOut

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