Phosphoglycerate kinase - Saccharomyces cerevisiae (Baker's yeast)

Names and origin

Protein names

Recommended name:
Phosphoglycerate kinase
EC=2.7.2.3

Gene names

Name:	PGK1
Ordered Locus Names:	YCR012W
ORF Names:	YCR12W

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

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General annotation (Comments)

Catalytic activity	ATP + 3-phospho-D-glycerate = ADP + 3-phospho-D-glyceroyl phosphate.
Pathway	Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5.
Subunit structure	Monomer.
Subcellular location	Cytoplasm.
Miscellaneous	Present with 314000 molecules/cell in log phase SD medium. Ref.10
Sequence similarities	Belongs to the phosphoglycerate kinase family.

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Ontologies

Keywords
Biological process	Glycolysis
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding
Molecular function	Kinase Transferase
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	gluconeogenesis Inferred from mutant phenotype. Source: SGD glycolysis Inferred from mutant phenotype. Source: SGD
Cellular component	mitochondrion Inferred from direct assay. Source: SGD plasma membrane enriched fraction Inferred from direct assay. Source: SGD
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW phosphoglycerate kinase activity Inferred from direct assay. Source: SGD
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

Removed

Chain

2 – 416

415

Phosphoglycerate kinase

PRO_0000145893

Regions

Nucleotide binding

371 – 374

4

ATP

Region

24 – 26

3

Substrate binding

Region

63 – 66

4

Substrate binding

Sites

Binding site

39

1

Substrate

Binding site

122

1

Substrate

Binding site

169

1

Substrate

Binding site

218

1

ATP

Binding site

311

1

ATP; via carbonyl oxygen

Binding site

335

1

ATP

Binding site

342

1

ATP

Amino acid modifications

Modified residue

2

1

N-acetylserine Ref.11

Modified residue

4

1

Phosphoserine Ref.11

Modified residue

5

1

Phosphoserine Ref.15

Modified residue

8

1

Phosphoserine Ref.15

Modified residue

36

1

Phosphoserine Ref.13

Modified residue

76

1

Phosphoserine Ref.15

Modified residue

93

1

Phosphothreonine Ref.15

Modified residue

110

1

Phosphoserine Ref.13

Modified residue

114

1

Phosphoserine Ref.15 Ref.13

Modified residue

130

1

Phosphoserine Ref.13

Modified residue

154

1

Phosphoserine Ref.12

Modified residue

203

1

Phosphothreonine Ref.15

Modified residue

241

1

Phosphothreonine Ref.15

Modified residue

331

1

Phosphothreonine Ref.15 Ref.12

Modified residue

376

1

Phosphothreonine Ref.15

Modified residue

391

1

Phosphoserine Ref.15 Ref.14

Modified residue

392

1

Phosphothreonine Ref.15 Ref.12

Modified residue

397

1

Phosphoserine Ref.13

Modified residue

413

1

Phosphoserine Ref.14

Experimental info

Mutagenesis

22

1

R → K: 2-fold reduction of Vmax. Ref.8

Mutagenesis

22

1

R → M: 7-fold reduction of Vmax. Ref.8

Sequence conflict

185

1

G → S AA sequence Ref.4

Sequence conflict

191

1

E → I AA sequence Ref.4

Secondary structure

1

.

416

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P00560-1 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 378AB944DB34EFF0
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FASTA

416

44,738

        10         20         30         40         50         60 
MSLSSKLSVQ DLDLKDKRVF IRVDFNVPLD GKKITSNQRI VAALPTIKYV LEHHPRYVVL 

        70         80         90        100        110        120 
ASHLGRPNGE RNEKYSLAPV AKELQSLLGK DVTFLNDCVG PEVEAAVKAS APGSVILLEN 

       130        140        150        160        170        180 
LRYHIEEEGS RKVDGQKVKA SKEDVQKFRH ELSSLADVYI NDAFGTAHRA HSSMVGFDLP 

       190        200        210        220        230        240 
QRAAGFLLEK ELKYFGKALE NPTRPFLAIL GGAKVADKIQ LIDNLLDKVD SIIIGGGMAF 

       250        260        270        280        290        300 
TFKKVLENTE IGDSIFDKAG AEIVPKLMEK AKAKGVEVVL PVDFIIADAF SADANTKTVT 

       310        320        330        340        350        360 
DKEGIPAGWQ GLDNGPESRK LFAATVAKAK TIVWNGPPGV FEFEKFAAGT KALLDEVVKS 

       370        380        390        400        410 
SAAGNTVIIG GGDTATVAKK YGVTDKISHV STGGGASLEL LEGKELPGVA FLSEKK

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The primary structure of the Saccharomyces cerevisiae gene for 3-phosphoglycerate kinase." Hitzeman R.A., Hagie F.E., Hayflick J.S., Chen C.Y., Seeburg P.H., Derynck R. Nucleic Acids Res. 10:7791-7808(1982) [PubMed: 6296791] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The complete sequence of a 10.8 kb segment distal of SUF2 on the right arm of chromosome III from Saccharomyces cerevisiae reveals seven open reading frames including the RVS161, ADP1 and PGK genes." Skala J., Purnelle B., Goffeau A. Yeast 8:409-417(1992) [PubMed: 1626432] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"The complete DNA sequence of yeast chromosome III." Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A., Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M. Sgouros J.G. Nature 357:38-46(1992) [PubMed: 1574125] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	"Structural studies on yeast 3-phosphoglycerate kinase. Linear arrangement of the CNBr fragments, partial amino acid sequence of the inner part of the polypeptide chain, and analyses of the N-terminal domain of the protein." Fattoum A., Roustan C., Karoui D., Feinberg J., Pradel L.-A., Gregoire J., Rochat H. Int. J. Pept. Protein Res. 17:393-400(1981) [PubMed: 7287307] [Abstract] Cited for: PROTEIN SEQUENCE OF 173-202 AND 238-270.
[5]	"The complete amino acid sequence of yeast phosphoglycerate kinase." Perkins R.E., Conroy S.C., Dunbar B., Fothergill L.A., Tuite M.F., Dobson M.J., Kingsman S.M., Kingsman A.J. Biochem. J. 211:199-218(1983) [PubMed: 6347186] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 282-416.
[6]	"Conservation of high efficiency promoter sequences in Saccharomyces cerevisiae." Dobson M.J., Tuite M.F., Roberts N.A., Kingsman A.J., Kingsman S.M., Perkins R.E., Conroy S.C., Dunbar B., Fothergill L.A. Nucleic Acids Res. 10:2625-2637(1982) [PubMed: 6281737] [Abstract] Cited for: PRELIMINARY PROTEIN SEQUENCE OF 268-398, NUCLEOTIDE SEQUENCE OF 2-7.
[7]	"Two-dimensional electrophoretic separation of yeast proteins using a non-linear wide range (pH 3-10) immobilized pH gradient in the first dimension; reproducibility and evidence for isoelectric focusing of alkaline (pI > 7) proteins." Norbeck J., Blomberg A. Yeast 13:1519-1534(1997) [PubMed: 9509572] [Abstract] Cited for: PROTEIN SEQUENCE OF 150-161; 198-209 AND 245-256. Strain: ATCC 44827 / SKQ2N.
[8]	"Characterisation of yeast phosphoglycerate kinase modified by mutagenesis at residue 21." Walker P.A., Joao H.C., Littlechild J.A., Wiliams R.J.P., Watson H.C. Eur. J. Biochem. 207:29-37(1992) [PubMed: 1628654] [Abstract] Cited for: MUTAGENESIS OF ARG-22.
[9]	"Yeast mitochondrial dehydrogenases are associated in a supramolecular complex." Grandier-Vazeille X., Bathany K., Chaignepain S., Camougrand N., Manon S., Schmitter J.-M. Biochemistry 40:9758-9769(2001) [PubMed: 11502169] [Abstract] Cited for: SUBCELLULAR LOCATION.
[10]	"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].
[11]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N. Mol. Cell. Proteomics 4:310-327(2005) [PubMed: 15665377] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, PHOSPHORYLATION AT SER-4, MASS SPECTROMETRY.
[12]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed: 17330950] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-154; THR-331 AND THR-392, MASS SPECTROMETRY.
[13]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed: 17287358] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-36; SER-110; SER-114; SER-130 AND SER-397, MASS SPECTROMETRY.
[14]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-391 AND SER-413, MASS SPECTROMETRY.
[15]	"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-5; SER-8; SER-76; THR-93; SER-114; THR-203; THR-241; THR-331; THR-376; SER-391 AND THR-392, MASS SPECTROMETRY.
[16]	"Sequence and structure of yeast phosphoglycerate kinase." Watson H.C., Walker N.P.C., Shaw P.J., Bryant T.N., Wendell P.L., Fothergill L.A., Perkins R.E., Conroy S.C., Dobson M.J., Tuite M.F., Kingsman A.J., Kingsman S.M. EMBO J. 1:1635-1640(1982) [PubMed: 6765200] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND ATP ANALOG.
[17]	"Structure of the R65Q mutant of yeast 3-phosphoglycerate kinase complexed with Mg-AMP-PNP and 3-phospho-D-glycerate." McPhillips T.M., Hsu B.T., Sherman M.A., Mas M.T., Rees D.C. Biochemistry 35:4118-4127(1996) [PubMed: 8672447] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF MUTANT GLN-66 IN COMPLEX WITH SUBSTRATE AND ATP ANALOG.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

J01342 Genomic DNA. Translation: AAA88729.1.
X59720 Genomic DNA. Translation: CAA42329.2.
M14438 Genomic DNA. Translation: AAA34864.1.
K00553 Genomic DNA. Translation: AAA34863.1. Sequence problems.

PIR

KIBYG. S19422.

RefSeq

NP_009938.2.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FW8	X-ray	2.30	A	2-416	[»]
1QPG	X-ray	2.40	A	2-416	[»]
3PGK	X-ray	2.50	A	2-416	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:4152N.

IntAct

P00560. 46 interactions.

STRING

P00560.

2-D gel databases

COMPLUYEAST-2DPAGE

P00560.

Proteomic databases

PeptideAtlas

P00560.

PRIDE

P00560.

Genome annotation databases

Ensembl

YCR012W; YCR012W; YCR012W; Saccharomyces cerevisiae. [Genome view]

GeneID

850370.

KEGG

sce:YCR012W.

NMPDR

fig|4932.3.peg.661.

Organism-specific databases

CYGD

YCR012w.

SGD

S000000605. PGK1.

Phylogenomic databases

HOGENOM

P00560.

OMA

KNELSYF

OrthoDB

EOG9908S2

Enzyme and pathway databases

BRENDA

2.7.2.3. 250.

Gene expression databases

ArrayExpress

P00560.

Genevestigator

P00560.

GermOnline

YCR012W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR001576. Phosphoglycerate_kinase.
IPR015901. Phosphoglycerate_kinase_C.
IPR015911. Phosphoglycerate_kinase_CS.
IPR015824. Phosphoglycerate_kinase_N.
[Graphical view]

Gene3D

G3DSA:3.40.50.1270. Phosphoglycerate_kinase_C. 1 hit.
G3DSA:3.40.50.1260. Phosphoglycerate_kinase_N. 1 hit.

PANTHER

PTHR11406. PGK. 1 hit.

Pfam

PF00162. PGK. 1 hit.
[Graphical view]

PRINTS

PR00477. PHGLYCKINASE.

PROSITE

PS00111. PGLYCERATE_KINASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

965861.

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Entry information

Entry name

PGK_YEAST

Accession

Primary (citable) accession number: P00560

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	November 24, 2009
This is version 111 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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