Glycerol-3-phosphate dehydrogenase [NAD(+)] 2, chloroplastic precursor

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Q949Q0 (GPDA2_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 97. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Glycerol-3-phosphate dehydrogenase [NAD(+)] 2, chloroplastic
EC=1.1.1.8

Alternative name(s):
Protein SUPPRESSOR OF FATTY ACID DESATURASE DEFICIENCY 1

Gene names

Name:	GLY1
Synonyms:	SFD1
Ordered Locus Names:	At2g40690

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	420 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Required to supply glycerol-3-phosphate in the chloroplast for the synthesis of glycerolipids. Required for activation of systemic acquired resistance (SAR). Provision of glycerol-3-phosphate may be involved in generating lipid signals necessary for mediating defense responses and SAR. Ref.4 Ref.5 Ref.6 Ref.7 Ref.8
Catalytic activity	sn-glycerol 3-phosphate + NAD⁺ = glycerone phosphate + NADH. Ref.4 Ref.5 Ref.8
Pathway	Membrane lipid metabolism; glycerophospholipid metabolism. HAMAP-Rule MF_00394
Subcellular location	Plastid › chloroplast By similarity.
Disruption phenotype	No visible phenotype under normal growth conditions, but leaves have decreased levels of hexadecatrienoic fatty acid (16:3) and increased levels of oleic acid (18:1). Ref.4 Ref.5
Sequence similarities	Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family.
Biophysicochemical properties	Kinetic parameters: K_M=0.33 µM for glycerone phosphate Ref.8 V_max=49 µmol/min/mg enzyme toward glycerone phosphate

Ontologies

Keywords
Biological process	Lipid biosynthesis Lipid metabolism Phospholipid biosynthesis Phospholipid metabolism Plant defense
Cellular component	Chloroplast Plastid
Domain	Transit peptide
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	carbohydrate metabolic process Inferred from electronic annotation. Source: InterPro glycerol-3-phosphate catabolic process Inferred from electronic annotation. Source: InterPro glycerolipid biosynthetic process Inferred from mutant phenotype PubMed 9662534. Source: TAIR glycerophospholipid metabolic process Inferred from electronic annotation. Source: UniProtKB-UniPathway phospholipid biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW systemic acquired resistance Inferred from mutant phenotype Ref.4. Source: TAIR
Cellular_component	chloroplast envelope Inferred from direct assay PubMed 20061580. Source: TAIR glycerol-3-phosphate dehydrogenase complex Inferred from electronic annotation. Source: InterPro
Molecular_function	NAD binding Inferred from electronic annotation. Source: InterPro glycerol-3-phosphate dehydrogenase [NAD+] activity Inferred from genetic interaction Ref.4. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 45

Chloroplast Potential

Chain

46 – 420

375

Glycerol-3-phosphate dehydrogenase [NAD(+)] 2, chloroplastic HAMAP-Rule MF_00394

PRO_0000420174

Regions

Nucleotide binding

94 – 99

NAD By similarity

Region

343 – 344

Substrate binding By similarity

Sites

Active site

279

Proton acceptor By similarity

Binding site

171

NAD By similarity

Binding site

194

NAD; via amide nitrogen By similarity

Binding site

194

Substrate By similarity

Binding site

228

NAD; via amide nitrogen By similarity

Binding site

343

NAD By similarity

Binding site

369

NAD By similarity

Experimental info

Mutagenesis

194

K → A: Loss of activity. Ref.8

Mutagenesis

279

K → A: Loss of activity. Ref.8

Mutagenesis

332

D → A: Loss of activity. Ref.8

Sequences

Sequence

Length

Mass (Da)

Tools

Q949Q0 [UniParc].

Last modified December 1, 2001. Version 1.
Checksum: 3AACC248276BFC01
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FASTA

420

45,092

        10         20         30         40         50         60 
MAASVQPACL DLHFSGKHPP LLKHNAIIVR CVSSPNVIPE ADSISGPPDI INTNRDQRKV 

        70         80         90        100        110        120 
VRIAWEKLVR WSRSLRAKAK TDVLERTRKV VVLGGGSFGT AMAAHVARRK EGLEVNMLVR 

       130        140        150        160        170        180 
DSFVCQSINE NHHNCKYFPE HKLPENVIAT TDAKAALLDA DYCLHAVPVQ FSSSFLEGIA 

       190        200        210        220        230        240 
DYVDPGLPFI SLSKGLELNT LRMMSQIIPI ALKNPRQPFV ALSGPSFALE LMNNLPTAMV 

       250        260        270        280        290        300 
VASKDKKLAN AVQQLLASSY LRINTSSDVT GVEIAGALKN VLAIAAGIVD GMNLGNNSMA 

       310        320        330        340        350        360 
ALVSQGCSEI RWLATKMGAK PTTITGLSGT GDIMLTCFVN LSRNRTVGVR LGSGETLDDI 

       370        380        390        400        410        420 
LTSMNQVAEG VATAGAVIAL AQKYNVKLPV LTAVAKIIDN ELTPTKAVLE LMNLPQIEEV

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana." Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D., Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V., Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S., Cronin L.A. Venter J.C. Nature 402:761-768(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[2]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[3]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. Ecker J.R. Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[4]	"The Arabidopsis thaliana dihydroxyacetone phosphate reductase gene SUPPRESSSOR OF FATTY ACID DESATURASE DEFICIENCY1 is required for glycerolipid metabolism and for the activation of systemic acquired resistance." Nandi A., Welti R., Shah J. Plant Cell 16:465-477(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE.
[5]	"Oleic acid levels regulated by glycerolipid metabolism modulate defense gene expression in Arabidopsis." Kachroo A., Venugopal S.C., Lapchyk L., Falcone D., Hildebrand D., Kachroo P. Proc. Natl. Acad. Sci. U.S.A. 101:5152-5157(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE.
[6]	"Plastidial fatty acid levels regulate resistance gene-dependent defense signaling in Arabidopsis." Chandra-Shekara A.C., Venugopal S.C., Barman S.R., Kachroo A., Kachroo P. Proc. Natl. Acad. Sci. U.S.A. 104:7277-7282(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"Plastid omega3-fatty acid desaturase-dependent accumulation of a systemic acquired resistance inducing activity in petiole exudates of Arabidopsis thaliana is independent of jasmonic acid." Chaturvedi R., Krothapalli K., Makandar R., Nandi A., Sparks A.A., Roth M.R., Welti R., Shah J. Plant J. 54:106-117(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[8]	"Biochemical and molecular-genetic characterization of SFD1's involvement in lipid metabolism and defense signaling." Lorenc-Kukula K., Chaturvedi R., Roth M., Welti R., Shah J. Front. Plant Sci. 3:26-26(2012) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF LYS-194; LYS-279 AND ASP-332.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP002685 Genomic DNA. Translation: AEC09864.1. AY050968 mRNA. Translation: AAK93645.1. AY114078 mRNA. Translation: AAM45126.1.
IPI	IPI00526002.
RefSeq	NP_565939.1. NM_129631.2.
UniGene	At.26537.
3D structure databases
HSSP	HSSP built from PDB template 1EVY based on UniProtKB P90551.
ProteinModelPortal	Q949Q0.
SMR	Q949Q0. Positions 89-412.
ModBase	Search...
Protein-protein interaction databases
STRING	3702.AT2G40690.1-P.
Proteomic databases
PaxDb	Q949Q0.
PRIDE	Q949Q0.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT2G40690.1; AT2G40690.1; AT2G40690.
GeneID	818664.
KEGG	ath:AT2G40690.
Organism-specific databases
TAIR	At2g40690.
Phylogenomic databases
eggNOG	COG0240.
HOGENOM	HOG000246853.
InParanoid	Q949Q0.
OMA	DVIGCEI.
PhylomeDB	Q949Q0.
ProtClustDB	CLSN2688847.
Enzyme and pathway databases
UniPathway	UPA00940.
Gene expression databases
Genevestigator	Q949Q0.
Family and domain databases
Gene3D	1.10.1040.10. 1 hit. 3.40.50.720. 1 hit.
HAMAP	MF_00394. NAD_Glyc3P_dehydrog.
InterPro	IPR008927. 6-PGluconate_DH_C-like. IPR013328. DH_multihelical. IPR006168. G3P_DH_NAD-dep. IPR006109. G3P_DH_NAD-dep_C. IPR011128. G3P_DH_NAD-dep_N. IPR016040. NAD(P)-bd_dom. [Graphical view]
PANTHER	PTHR11728. PTHR11728. 1 hit.
Pfam	PF07479. NAD_Gly3P_dh_C. 1 hit. PF01210. NAD_Gly3P_dh_N. 1 hit. [Graphical view]
PIRSF	PIRSF000114. Glycerol-3-P_dh. 1 hit.
PRINTS	PR00077. GPDHDRGNASE.
SUPFAM	SSF48179. 6DGDH_C_like. 1 hit.
PROSITE	PS00957. NAD_G3PDH. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

GPDA2_ARATH

Accession

Primary (citable) accession number: Q949Q0

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 28, 2012
Last sequence update:	December 1, 2001
Last modified:	May 1, 2013
This is version 97 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program

Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents