PDX2 pyridoxine biosynthesis 2 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: PDX2
Official Full Name: pyridoxine biosynthesis 2
Primary source: TAIR:AT5G60540
Locus tag: AT5G60540
See related: Araport:AT5G60540
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: ATPDX2; EMB2407; EMBRYO DEFECTIVE 2407; MUF9.1; MUF9_1; pyridoxine biosynthesis 2; PYRIDOXINE BIOSYNTHESIS 2
Summary: Encodes a protein predicted to function in tandem with PDX1 to form glutamine amidotransferase complex with involved in vitamin B6 biosynthesis. PDX2 is predicted to function as glutaminase within the complex.
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Genomic context

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See PDX2 in Genome Data Viewer

Location:: chromosome: 5

Exon count:: 6

Sequence:: Chromosome: 5; NC_003076.8 (24336623..24338802, complement)

Chromosome 5 - NC_003076.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003076.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PDX proteins from Arabidopsis thaliana as novel substrates of cathepsin B: implications for vitamin B6 biosynthesis regulation.
Title: PDX proteins from Arabidopsis thaliana as novel substrates of cathepsin B: implications for vitamin B(6) biosynthesis regulation.
Based on a model of the PDX1/PDX2 complex, mutation of a single residue uncouples enzyme coordination and in turn provides tangible evidence for the existence of the recently proposed ammonia tunnel through the core of PDX1.
Title: Functional analysis of PDX2 from Arabidopsis, a glutaminase involved in vitamin B6 biosynthesis.

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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

Orthologs from OrthoDB

NM_125447.2

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables glutaminase activity	IDA Inferred from Direct Assay more info	PubMed
enables glutaminase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables protein heterodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within embryo development ending in seed dormancy	NAS Non-traceable Author Statement more info
involved_in pyridoxal phosphate biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within vitamin B6 biosynthetic process	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within vitamin B6 biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	ISM Inferred from Sequence Model more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: pyridoxine biosynthesis 2

NP_568922.1

pyridoxine biosynthesis 2 (PDX2); CONTAINS InterPro DOMAIN/s: PdxT/SNO family, conserved site (InterPro:IPR021196), SNO glutamine amidotransferase (InterPro:IPR002161); 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

NC_003076.8 Reference assembly

Range

24336623..24338802 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_125447.2 → NP_568922.1 pyridoxine biosynthesis 2 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_568922.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q56ZP9, Q8LAD0, Q9FKJ3

UniProtKB/TrEMBL

A0A178UA48, A0A5S9YFS5, F2XYF7

Conserved Domains (1) summary

PLN02832
Location:1 → 255

PLN02832; glutamine amidotransferase subunit of pyridoxal 5'-phosphate synthase complex