O04130 (SERA_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
D-3-phosphoglycerate dehydrogenase, chloroplastic
Short name=3-PGDH
EC=1.1.1.95

Gene names

Ordered Locus Names:	At1g17745
ORF Names:	F11A6.8

Organism

Arabidopsis thaliana (Mouse-ear cress)

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	624 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)

Catalytic activity	3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH. 2-hydroxyglutarate + NAD+ = 2-oxoglutarate + NADH.
Pathway	Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 1/3.
Subcellular location	Plastid › chloroplast.
Sequence similarities	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. Contains 1 ACT domain.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Serine biosynthesis
Cellular component	Chloroplast Plastid
Coding sequence diversity	Alternative splicing
Domain	Transit peptide
Ligand	NAD
Molecular function	Oxidoreductase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	L-serine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	chloroplast stroma Inferred from direct assay. Source: TAIR cytosol Inferred from direct assay Ref.6. Source: TAIR nucleus Inferred from direct assay Ref.6. Source: TAIR
Molecular function	NAD binding Inferred from electronic annotation. Source: InterPro amino acid binding Inferred from electronic annotation. Source: InterPro phosphoglycerate dehydrogenase activity Inferred from electronic annotation. Source: EC protein binding Inferred from physical interaction. Source: TAIR
Complete GO annotation...

Alternative products

This entry describes 1 isoform produced by alternative splicing. [Select]

Note: A number of isoforms are produced. According to EST sequences.

Isoform 1 (identifier: O04130-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 49	49	Chloroplast Potential
	Chain	50 – 624	575	D-3-phosphoglycerate dehydrogenase, chloroplastic		PRO_0000007192
Regions
	Domain	551 – 621	71	ACT
	Nucleotide binding	231 – 232	2	NAD By similarity
	Nucleotide binding	310 – 312	3	NAD By similarity
	Nucleotide binding	360 – 363	4	NAD By similarity
Sites
	Active site	312	1	By similarity
	Active site	341	1	By similarity
	Active site	360	1	Proton donor By similarity
	Binding site	251	1	NAD By similarity
	Binding site	336	1	NAD By similarity
Amino acid modifications
	Modified residue	71	1	Phosphoserine Ref.6 Ref.7 Ref.8

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified January 1, 1998. Version 2. Checksum: 724370F870DEA310	FASTA	624	66,454
	10 20 30 40 50 60 MAFSSSCSSV KAVNSRWTSP SPSPSSRFAV LPAFLHRRYA TSVKLTAISA ALKTVEQTTL 70 80 90 100 110 120 TEDNRFSTVG SDSDEYNPTL PKPRILVTEK LGEAGVNLLR EFGDVDCSYD LSPEDLKKKV 130 140 150 160 170 180 AESDALIVRS GTKVTREVFE AAKGRLKVVG RAGVGIDNVD LQAATEHGCL VVNAPTANTV 190 200 210 220 230 240 AAAEHGIALL ASMARNVAQA DASIKAGKWE RSKYVGVSLV GKTLAVMGFG KVGTEVARRA 250 260 270 280 290 300 KGLGMTVISH DPYAPADRAR ALGVDLVSFD QAISTADFVS LHMPLTPATK KVFNDETFSK 310 320 330 340 350 360 MKKGVRLINV ARGGVIDEDA LVRALDAGIV AQAALDVFCE EPPSKDSRLI QHENVTVTPH 370 380 390 400 410 420 LGASTKEAQE GVAIEIAEAV AGALKGELSA TAVNAPMVAP EVLSELTPYI VLAEKLGRLA 430 440 450 460 470 480 VQLASGGKGV QSIRVVYRSA RDRDDLDTRL LRAMITKGII EPISDSYVNL VNADFIAKQK 490 500 510 520 530 540 GLRISEERMV VDSSPEYPVD SIQVQILNVE SNFAGAVSDA GDISIEGKVK YGVPHLTCVG 550 560 570 580 590 600 SFGVDVSLEG NLILCRQVDQ PGMIGQVGNI LGEQNVNVNF MSVGRTVLRK QAIMAIGVDE 610 620 EPDNKTLERI GGVSAIEEFV FLKL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Regulation of serine biosynthesis in Arabidopsis. Crucial role of plastidic 3-phosphoglycerate dehydrogenase in non-photosynthetic tissues." Ho C.-L., Noji M., Saito M., Saito K. J. Biol. Chem. 274:397-402(1999) [PubMed: 9867856] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
[2]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [PubMed: 11130712] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"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. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed: 14593172] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"Full-length cDNA from Arabidopsis thaliana." Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A. Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[6]	"Site-specific phosphorylation profiling of Arabidopsis proteins by mass spectrometry and peptide chip analysis." de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E., Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J., Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H. J. Proteome Res. 7:2458-2470(2008) [PubMed: 18433157] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-71, MASS SPECTROMETRY. Tissue: Root.
[7]	"Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana." Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E., Rathjen J.P., Peck S.C. J. Proteomics 72:439-451(2009) [PubMed: 19245862] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-71, MASS SPECTROMETRY. Strain: cv. Columbia.
[8]	"Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks." Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S. Plant Physiol. 150:889-903(2009) [PubMed: 19376835] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-71, MASS SPECTROMETRY. Strain: cv. Columbia. Tissue: Seedling.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AB003280 mRNA. Translation: BAA20405.1. AB010407 Genomic DNA. Translation: BAA24440.1. AC034257 Genomic DNA. Translation: AAF99816.1. CP002684 Genomic DNA. Translation: AEE29630.1. AY050399 mRNA. Translation: AAK91415.1. AY098953 mRNA. Translation: AAM19963.1. AY086001 mRNA. Translation: AAM63210.1.
IPI	IPI00547060.
PIR	T52296.
RefSeq	NP_564034.1. NM_101636.2.
UniGene	At.21252. At.73011.
3D structure databases
ProteinModelPortal	O04130.
SMR	O04130. Positions 81-622.
ModBase	Search...
Protein-protein interaction databases
IntAct	O04130. 1 interaction.
STRING	O04130.
Proteomic databases
PRIDE	O04130.
ProMEX	O04130.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT1G17745.1; AT1G17745.1; AT1G17745.
GeneID	838352.
GenomeReviews	Gene locus AT1G17745 in contig CT485782_GR.
KEGG	ath:AT1G17745.
NMPDR	fig|3702.1.peg.2102.
Organism-specific databases
TAIR	At1g17745.
Phylogenomic databases
eggNOG	KOG0068.
GeneTree	EPGT00050000011788.
HOGENOM	HBG731446.
InParanoid	O04130.
OMA	AEHTVAM.
PhylomeDB	O04130.
ProtClustDB	CLSN2685732.
Gene expression databases
Genevestigator	O04130.
GermOnline	AT1G17745. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR002912. ACT-bd. IPR006236. D-3-Phosphoglycerate_DH. IPR006139. D-isomer_2_OHA_DH_cat_dom. IPR006140. D-isomer_2_OHA_DH_NAD-bd. IPR016040. NAD(P)-bd_dom. [Graphical view]
Gene3D	G3DSA:3.40.50.720. NAD(P)-bd. 2 hits.
KO	K00058.
PANTHER	PTHR10996:SF20. D3PG_Deh. 1 hit.
Pfam	PF00389. 2-Hacid_dh. 1 hit. PF02826. 2-Hacid_dh_C. 1 hit. PF01842. ACT. 1 hit. [Graphical view]
TIGRFAMs	TIGR01327. PGDH. 1 hit.
PROSITE	PS00065. D_2_HYDROXYACID_DH_1. 1 hit. PS00670. D_2_HYDROXYACID_DH_2. 1 hit. PS00671. D_2_HYDROXYACID_DH_3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

SERA_ARATH

Accession

Primary (citable) accession number: O04130

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	January 1, 1998
Last modified:	January 25, 2012
This is version 105 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program