P40054 (SERA_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
D-3-phosphoglycerate dehydrogenase 1
Short name=3-PGDH 1
EC=1.1.1.95

Gene names

Name:	SER3
Ordered Locus Names:	YER081W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	469 AA.
Sequence status	Complete.
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.
Miscellaneous	Present with 7670 molecules/cell in log phase SD medium. Ref.3
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
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	cytoplasm Inferred from direct assay. Source: SGD
Molecular function	NAD binding Inferred from electronic annotation. Source: InterPro phosphoglycerate dehydrogenase activity Inferred from mutant phenotype. Source: SGD protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
SER33	P40510	4	EBI-16961,EBI-16821

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 469	469	D-3-phosphoglycerate dehydrogenase 1		PRO_0000076018
Regions
	Domain	398 – 468	71	ACT
	Nucleotide binding	208 – 209	2	NAD By similarity
	Nucleotide binding	285 – 287	3	NAD By similarity
	Nucleotide binding	347 – 350	4	NAD By similarity
Sites
	Active site	287	1	By similarity
	Active site	316	1	By similarity
	Active site	347	1	Proton donor By similarity
	Binding site	228	1	NAD By similarity
	Binding site	311	1	NAD By similarity
Amino acid modifications
	Modified residue	20	1	Phosphoserine Ref.4
	Modified residue	22	1	Phosphoserine Ref.4
	Modified residue	29	1	Phosphoserine Ref.4

Sequences

	Sequence		Length	Mass (Da)
	P40054 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: E1E69070BF41A87C	FASTA	469	51,193
	10 20 30 40 50 60 MTSIDINNLQ NTFQQAMNMS GSPGAVCTSP TQSFMNTVPQ RLNAVKHPKI LKPFSTGDMK 70 80 90 100 110 120 ILLLENVNQT AITIFEEQGY QVEFYKSSLP EEELIEKIKD VHAIGIRSKT RLTSNVLQHA 130 140 150 160 170 180 KNLVCIGCFC IGTNQVDLDY ATSRGIAVFN SPFSNSRSVA ELVIAEIISL ARQLGDRSIE 190 200 210 220 230 240 LHTGTWNKVA ARCWEVRGKT LGIIGYGHIG SQLSVLAEAM GLHVLYYDIV TIMALGTARQ 250 260 270 280 290 300 VSTLDELLNK SDFVTLHVPA TPETEKMLSA PQFAAMKDGA YVINASRGTV VDIPSLIQAV 310 320 330 340 350 360 KANKIAGAAL DVYPHEPAKN GEGSFNDELN SWTSELVSLP NIILTPHIGG STEEAQSSIG 370 380 390 400 410 420 IEVATALSKY INEGNSVGSV NFPEVALKSL SYDQENTVRV LYIHQNVPGV LKTVNDILSN 430 440 450 460 HNIEKQFSDS NGEIAYLMAD ISSVDQSDIK DIYEQLNQTS AKISIRLLY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome V." Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. , Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y., Botstein D., Davis R.W. Nature 387:78-81(1997) [PubMed: 9169868] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[4]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-20; SER-22 AND SER-29, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U18839 Genomic DNA. Translation: AAB64636.1. BK006939 Genomic DNA. Translation: DAA07742.1.
PIR	S50584.
RefSeq	NP_011004.1. NM_001178972.1.
3D structure databases
ProteinModelPortal	P40054.
SMR	P40054. Positions 53-469.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-5336N.
IntAct	P40054. 21 interactions.
MINT	MINT-404076.
STRING	P40054.
Proteomic databases
PeptideAtlas	P40054.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YER081W; YER081W; YER081W.
GeneID	856814.
KEGG	sce:YER081W.
NMPDR	fig|4932.3.peg.2074.
Organism-specific databases
CYGD	YER081w.
SGD	S000000883. SER3.
Phylogenomic databases
eggNOG	fuNOG05789.
GeneTree	EFGT00050000001276.
HOGENOM	HBG731446.
OMA	ESANCHE.
OrthoDB	EOG4NGKWJ.
Gene expression databases
ArrayExpress	P40054.
Genevestigator	P40054.
GermOnline	YER081W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	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.
Pfam	PF00389. 2-Hacid_dh. 1 hit. PF02826. 2-Hacid_dh_C. 1 hit. [Graphical view]
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...
Other
NextBio	983085.

Entry information

Entry name

SERA_YEAST

Accession

Primary (citable) accession number: P40054
Secondary accession number(s): D3DLY8

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	December 14, 2011
This is version 112 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program