D-3-phosphoglycerate dehydrogenase 1 - Saccharomyces cerevisiae (Baker's yeast)

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Reviewed, UniProtKB/Swiss-Prot P40054 (SERA_YEAST)

Last modified June 16, 2009. Version 86. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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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 (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

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

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Protein attributes

Sequence length	469 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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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-glyceric acid: step 1/3.
Miscellaneous	Present with 7670 molecules/cell in log phase SD medium. Ref.2
Sequence similarities	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. Contains 1 ACT domain.

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Ontologies

Keywords
Biological process	Amino-acid biosynthesis Serine biosynthesis
Ligand	NAD
Molecular function	Oxidoreductase
PTM	Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	L-serine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from direct assay. Source: SGD
Molecular function	NAD or NADH binding Inferred from electronic annotation. Source: InterPro amino acid binding Inferred from electronic annotation. Source: InterPro identical protein binding Inferred from physical interaction. Source: IntAct phosphoglycerate dehydrogenase activity Inferred from mutant phenotype. Source: SGD
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct
itself		1	EBI-16961,EBI-16961
	O13567	1	EBI-16961,EBI-38884
	O13569	1	EBI-16961,EBI-37420
	Q99318	1	EBI-16961,EBI-34201
BDH1	P39714	1	EBI-16961,EBI-3501
CNS1	P33313	1	EBI-16961,EBI-4806
CST26	P38226	1	EBI-16961,EBI-21429
MAF1	P41910	1	EBI-16961,EBI-10375
MSS116	P15424	1	EBI-16961,EBI-11308
NSL1	Q12143	1	EBI-16961,EBI-33666
NUP42	P49686	1	EBI-16961,EBI-12310
RNR2	P09938	1	EBI-16961,EBI-15240
SER33	P40510	1	EBI-16961,EBI-16821
SFA1	P32771	1	EBI-16961,EBI-6770
TMS1	Q12116	1	EBI-16961,EBI-19306
TY1B-NL2	Q99337	1	EBI-16961,EBI-34960

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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

ACT

Sites

Active site

287

By similarity

Active site

316

By similarity

Active site

347

Proton donor By similarity

Amino acid modifications

Modified residue

Phosphoserine Ref.3

Modified residue

Phosphoserine Ref.3

Modified residue

Phosphoserine Ref.3

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Sequences

Sequence

Length

Mass (Da)

Tools

P40054-1 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: E1E69070BF41A87C
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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

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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. 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]	"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].
[3]	"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.

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Cross-references

Sequence databases
	U18839 Genomic DNA. Translation: AAB64636.1.
PIR	S50584.
RefSeq	NP_011004.1.
3D structure databases
HSSP	HSSP built from PDB template 1PSD based on UniProtKB P08328.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP:5336N.
IntAct	P40054. 97 interactions.
Proteomic databases
PeptideAtlas	P40054.
PRIDE	P40054.
Genome annotation databases
Ensembl	YER081W. Saccharomyces cerevisiae. [Contig view]
GeneID	856814.
GenomeReviews	Gene locus YER081W in contig U00092_GR.
KEGG	sce:YER081W.
NMPDR	fig\|4932.3.peg.2074.
Organism-specific databases
CYGD	YER081w.
SGD	S000000883. SER3.
Yeast-GFP	Search...
Phylogenomic databases
HOGENOM	P40054.
OMA	P40054. TEGELGY.
Enzyme and pathway databases
BRENDA	1.1.1.95. 250.
Gene expression databases
GermOnline	YER081W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR002912. ACT_bd. IPR006139. D-isomer_2_OHA_DH. IPR006140. D-isomer_2_OHA_DH_NAD-bd. IPR016040. NAD(P)-bd_dom. [Graphical view]
Gene3D	G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.
Pfam	PF00389. 2-Hacid_dh. 1 hit. PF02826. 2-Hacid_dh_C. 1 hit. PF01842. ACT. 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 Resources
NextBio	983085.

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Entry information

Entry name

SERA_YEAST

Accession

Primary (citable) accession number: P40054

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	June 16, 2009
This is version 86 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome V

Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents