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P00560 (PGK_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 148. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Phosphoglycerate kinase

EC=2.7.2.3
Gene names
Name:PGK1
Ordered Locus Names:YCR012W
ORF Names:YCR12W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length416 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

ATP + 3-phospho-D-glycerate = ADP + 3-phospho-D-glyceroyl phosphate. HAMAP-Rule MF_00145

Pathway

Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5. HAMAP-Rule MF_00145

Subunit structure

Monomer.

Subcellular location

Cytoplasm Ref.10.

Miscellaneous

Present with 314000 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the phosphoglycerate kinase family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.12
Chain2 – 416415Phosphoglycerate kinase HAMAP-Rule MF_00145
PRO_0000145893

Regions

Nucleotide binding371 – 3744ATP HAMAP-Rule MF_00145
Region24 – 263Substrate binding HAMAP-Rule MF_00145
Region63 – 664Substrate binding HAMAP-Rule MF_00145

Sites

Binding site391Substrate
Binding site1221Substrate
Binding site1691Substrate
Binding site2181ATP
Binding site3111ATP; via carbonyl oxygen
Binding site3351ATP
Binding site3421ATP

Amino acid modifications

Modified residue21N-acetylserine Ref.12 Ref.17
Modified residue931Phosphothreonine Ref.15
Modified residue1101Phosphoserine Ref.16
Modified residue1301Phosphoserine Ref.14
Modified residue1541Phosphoserine Ref.13
Modified residue1721Phosphoserine Ref.16
Modified residue2031Phosphothreonine Ref.15
Modified residue2411Phosphothreonine Ref.15
Modified residue2981Phosphothreonine Ref.16
Modified residue3181Phosphoserine Ref.16
Modified residue3311Phosphothreonine Ref.13 Ref.15 Ref.16
Modified residue3921Phosphothreonine Ref.13 Ref.16

Experimental info

Mutagenesis221R → K: 2-fold reduction of Vmax. Ref.9
Mutagenesis221R → M: 7-fold reduction of Vmax. Ref.9
Sequence conflict1851G → S AA sequence Ref.5
Sequence conflict1911E → I AA sequence Ref.5

Secondary structure

..................................................................................... 416
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P00560 [UniParc].

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

FASTA41644,738
        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 

« Hide

References

« Hide '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] [Europe PMC] [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] [Europe PMC] [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. expand/collapse author list , Carcano C., Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M., Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C., Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C., Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E., Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P., Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P., Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M., Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P., Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G., Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E., Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F., Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L., Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J., Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M., Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A., Richterich P., Roberts A.B., Rodriguez F., Sanz E., Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J., Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I., Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M., Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M., Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D., Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K., Sgouros J.G.
Nature 357:38-46(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"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] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 173-202 AND 238-270.
[6]"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 282-416.
[7]"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] [Europe PMC] [Abstract]
Cited for: PRELIMINARY PROTEIN SEQUENCE OF 268-398, NUCLEOTIDE SEQUENCE OF 2-7.
[8]"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] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 150-161; 198-209 AND 245-256.
Strain: ATCC 44827 / SKQ2N.
[9]"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] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF ARG-22.
[10]"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] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[11]"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] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[12]"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] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
Strain: YAL6B.
[13]"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] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-154; THR-331 AND THR-392, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Strain: ADR376.
[14]"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] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-130, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[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] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-93; THR-203; THR-241 AND THR-331, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[16]"Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-110; SER-172; THR-298; SER-318; THR-331 AND THR-392, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[17]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[18]"Sites of ubiquitin attachment in Saccharomyces cerevisiae."
Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[19]"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] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND ATP ANALOG.
[20]"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] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF MUTANT GLN-66 IN COMPLEX WITH SUBSTRATE AND ATP ANALOG.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
BK006937 Genomic DNA. Translation: DAA07490.1.
PIRKIBYG. S19422.
RefSeqNP_009938.2. NM_001178725.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1FW8X-ray2.30A2-416[»]
1QPGX-ray2.40A2-416[»]
3PGKX-ray2.50A2-416[»]
ProteinModelPortalP00560.
SMRP00560. Positions 2-416.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid30991. 82 interactions.
DIPDIP-4152N.
IntActP00560. 45 interactions.
MINTMINT-484961.
STRING4932.YCR012W.

Chemistry

BindingDBP00560.
ChEMBLCHEMBL2674.

2D gel databases

COMPLUYEAST-2DPAGEP00560.

Proteomic databases

PaxDbP00560.
PeptideAtlasP00560.
PRIDEP00560.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYCR012W; YCR012W; YCR012W.
GeneID850370.
KEGGsce:YCR012W.

Organism-specific databases

SGDS000000605. PGK1.

Phylogenomic databases

eggNOGCOG0126.
GeneTreeENSGT00390000008820.
HOGENOMHOG000227107.
KOK00927.
OMAGLDCGEK.
OrthoDBEOG71K6D7.

Enzyme and pathway databases

BioCycYEAST:YCR012W-MONOMER.
SABIO-RKP00560.
UniPathwayUPA00109; UER00185.

Gene expression databases

GenevestigatorP00560.

Family and domain databases

Gene3D3.40.50.1260. 1 hit.
3.40.50.1270. 1 hit.
HAMAPMF_00145. Phosphoglyc_kinase.
InterProIPR001576. Phosphoglycerate_kinase.
IPR015901. Phosphoglycerate_kinase_C.
IPR015911. Phosphoglycerate_kinase_CS.
IPR015824. Phosphoglycerate_kinase_N.
[Graphical view]
PANTHERPTHR11406. PTHR11406. 1 hit.
PfamPF00162. PGK. 1 hit.
[Graphical view]
PIRSFPIRSF000724. Pgk. 1 hit.
PRINTSPR00477. PHGLYCKINASE.
SUPFAMSSF53748. SSF53748. 1 hit.
PROSITEPS00111. PGLYCERATE_KINASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP00560.
NextBio965861.
PROP00560.

Entry information

Entry namePGK_YEAST
AccessionPrimary (citable) accession number: P00560
Secondary accession number(s): D6VR21
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: March 19, 2014
This is version 148 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome III

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

Yeast

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

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways