EDA9 D-3-phosphoglycerate dehydrogenase [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: EDA9
Official Full Name: D-3-phosphoglycerate dehydrogenase
Primary source: TAIR:AT4G34200
Locus tag: AT4G34200
See related: Araport:AT4G34200
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: embryo sac development arrest 9; F10M10.7; PGDH1; phosphoglycerate dehydrogenase 1
Summary: Encodes a 3-phosphoglycerate dehydrogenase that is essential for embryo and pollen development.
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Genomic context

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See EDA9 in Genome Data Viewer

Location:: chromosome: 4

Exon count:: 4

Sequence:: Chromosome: 4; NC_003075.7 (16373731..16376666, complement)

Chromosome 4 - NC_003075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003075.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PGDH1 is essential for Arabidopsis development.
Title: Arabidopsis phosphoglycerate dehydrogenase1 of the phosphoserine pathway is essential for development and required for ammonium assimilation and tryptophan biosynthesis.
Genetic and molecular evidence were provided for the essential role of EDA9 for embryo and pollen development.
Title: Identification of the phosphoglycerate dehydrogenase isoform EDA9 as the essential gene for embryo and male gametophyte development in Arabidopsis.
Data indicate that 3-phosphoglycerate dehydrogenases PGDH (At1g17745) and EDA9 (At4g34200) were expressed preferentially in roots while 3-PGDH (At3g19480) was expressed mainly in the aerial parts and was not expressed or very poorly in roots.
Title: Functional characterization of the plastidial 3-phosphoglycerate dehydrogenase family in Arabidopsis.

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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_119583.4

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables ATP binding	HDA more info	PubMed
enables NAD binding	IEA Inferred from Electronic Annotation more info
enables phosphoglycerate dehydrogenase activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in L-serine biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryo development ending in seed dormancy	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within megagametogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pollen development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within sulfur amino acid metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chloroplast	HDA more info	PubMed
located_in chloroplast	ISM Inferred from Sequence Model more info
located_in chloroplast stroma	HDA more info	PubMed
NOT located_in cytosol	RCA inferred from Reviewed Computational Analysis more info	PubMed
located_in mitochondrion	HDA more info	PubMed
located_in plasma membrane	HDA more info	PubMed
located_in plastid	HDA more info	PubMed
located_in plastid	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: D-3-phosphoglycerate dehydrogenase

NP_195146.1

embryo sac development arrest 9 (EDA9); FUNCTIONS IN: ATP binding; INVOLVED IN: megagametogenesis; LOCATED IN: mitochondrion, chloroplast, membrane; EXPRESSED IN: 26 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: D-3-phosphoglycerate dehydrogenase (InterPro:IPR006236), D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (InterPro:IPR006139), D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (InterPro:IPR006140), D-3-phosphogylcerate Dehydrogenase (InterPro:IPR015508), Amino acid-binding ACT (InterPro:IPR002912), NAD(P)-binding domain (InterPro:IPR016040); BEST Arabidopsis thaliana protein match is: D-3-phosphoglycerate dehydrogenase (TAIR:AT3G19480.1); Has 30608 Blast hits to 30602 proteins in 2772 species: Archae - 489; Bacteria - 18520; Metazoa - 741; Fungi - 1175; Plants - 586; Viruses - 5; Other Eukaryotes - 9092 (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_003075.7 Reference assembly

Range

16373731..16376666 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_119583.4 → NP_195146.1 D-3-phosphoglycerate dehydrogenase [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_195146.1

Status: REVIEWED

UniProtKB/Swiss-Prot

O49485, Q8LGJ6

UniProtKB/TrEMBL

A0A178UWV4, A0A5S9Y0P4

Conserved Domains (1) summary

PRK13581
Location:62 → 603

PRK13581; D-3-phosphoglycerate dehydrogenase; Provisional