Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Phosphoglycerate kinase

Gene

PGK1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

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

Pathwayi: glycolysis

This protein is involved in step 2 of the subpathway that synthesizes pyruvate from D-glyceraldehyde 3-phosphate.
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. Glyceraldehyde-3-phosphate dehydrogenase 1 (TDH1), Glyceraldehyde-3-phosphate dehydrogenase 2 (TDH2), Glyceraldehyde-3-phosphate dehydrogenase 3 (TDH3)
  2. Phosphoglycerate kinase (PGK1)
  3. Phosphoglycerate mutase 2 (GPM2), Phosphoglycerate mutase 3 (GPM3), Phosphoglycerate mutase 1 (GPM1)
  4. Enolase 2 (ENO2), Enolase-related protein 2 (ERR2), Enolase-related protein 1 (ERR1), Enolase-related protein 3 (ERR3), Enolase 1 (ENO1)
  5. Pyruvate kinase 2 (PYK2), Pyruvate kinase 1 (CDC19)
This subpathway is part of the pathway glycolysis, which is itself part of Carbohydrate degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyruvate from D-glyceraldehyde 3-phosphate, the pathway glycolysis and in Carbohydrate degradation.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei39Substrate2 Publications1
Binding sitei122Substrate2 Publications1
Binding sitei169Substrate2 Publications1
Binding sitei218ATP1
Binding sitei311ATP; via carbonyl oxygen1
Binding sitei335ATP1
Binding sitei342ATP1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi371 – 374ATP4

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • phosphoglycerate kinase activity Source: SGD

GO - Biological processi

  • gluconeogenesis Source: SGD
  • glycolytic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Glycolysis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:YCR012W-MONOMER.
BRENDAi2.7.2.3. 984.
ReactomeiR-SCE-70171. Glycolysis.
R-SCE-70263. Gluconeogenesis.
SABIO-RKP00560.
UniPathwayiUPA00109; UER00185.

Names & Taxonomyi

Protein namesi
Recommended name:
Phosphoglycerate kinase (EC:2.7.2.3)
Gene namesi
Name:PGK1
Ordered Locus Names:YCR012W
ORF Names:YCR12W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome III

Organism-specific databases

EuPathDBiFungiDB:YCR012W.
SGDiS000000605. PGK1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • mitochondrion Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi22R → K: 2-fold reduction of Vmax. 1 Publication1
Mutagenesisi22R → M: 7-fold reduction of Vmax. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL2674.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00001458932 – 416Phosphoglycerate kinaseAdd BLAST415

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Cross-linki82Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei93PhosphothreonineCombined sources1
Modified residuei110PhosphoserineCombined sources1
Modified residuei130PhosphoserineCombined sources1
Modified residuei154PhosphoserineCombined sources1
Modified residuei172PhosphoserineCombined sources1
Cross-linki197Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei203PhosphothreonineCombined sources1
Modified residuei241PhosphothreonineCombined sources1
Cross-linki258Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki274Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei298PhosphothreonineCombined sources1
Cross-linki302Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei318PhosphoserineCombined sources1
Modified residuei331PhosphothreonineCombined sources1
Modified residuei392PhosphothreonineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP00560.
PRIDEiP00560.
TopDownProteomicsiP00560.

2D gel databases

COMPLUYEAST-2DPAGEP00560.

PTM databases

iPTMnetiP00560.

Interactioni

Subunit structurei

Monomer.2 Publications

Protein-protein interaction databases

BioGridi30991. 84 interactors.
DIPiDIP-4152N.
IntActiP00560. 46 interactors.
MINTiMINT-484961.

Chemistry databases

BindingDBiP00560.

Structurei

Secondary structure

1416
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi9 – 11Combined sources3
Beta strandi18 – 22Combined sources5
Beta strandi29 – 35Combined sources7
Helixi38 – 51Combined sources14
Beta strandi56 – 61Combined sources6
Beta strandi69 – 72Combined sources4
Helixi73 – 75Combined sources3
Helixi78 – 88Combined sources11
Beta strandi92 – 94Combined sources3
Beta strandi98 – 100Combined sources3
Helixi101 – 108Combined sources8
Beta strandi110 – 112Combined sources3
Beta strandi114 – 117Combined sources4
Helixi121 – 123Combined sources3
Turni125 – 128Combined sources4
Beta strandi129 – 133Combined sources5
Beta strandi136 – 139Combined sources4
Helixi142 – 153Combined sources12
Beta strandi157 – 161Combined sources5
Helixi164 – 166Combined sources3
Helixi172 – 175Combined sources4
Beta strandi182 – 184Combined sources3
Helixi186 – 200Combined sources15
Beta strandi204 – 211Combined sources8
Turni216 – 218Combined sources3
Helixi219 – 226Combined sources8
Beta strandi230 – 235Combined sources6
Helixi236 – 238Combined sources3
Helixi239 – 246Combined sources8
Helixi247 – 252Combined sources6
Helixi258 – 273Combined sources16
Beta strandi277 – 279Combined sources3
Beta strandi282 – 291Combined sources10
Beta strandi296 – 300Combined sources5
Turni301 – 303Combined sources3
Beta strandi304 – 306Combined sources3
Beta strandi310 – 314Combined sources5
Helixi316 – 328Combined sources13
Beta strandi330 – 336Combined sources7
Helixi344 – 346Combined sources3
Helixi348 – 362Combined sources15
Beta strandi366 – 369Combined sources4
Helixi373 – 380Combined sources8
Helixi384 – 386Combined sources3
Beta strandi387 – 390Combined sources4
Helixi395 – 401Combined sources7
Helixi407 – 410Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1FW8X-ray2.30A74-416[»]
1QPGX-ray2.40A2-416[»]
3PGKX-ray2.50A2-416[»]
ProteinModelPortaliP00560.
SMRiP00560.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00560.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni24 – 26Substrate binding3
Regioni63 – 66Substrate binding4

Sequence similaritiesi

Belongs to the phosphoglycerate kinase family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000008820.
HOGENOMiHOG000227107.
InParanoidiP00560.
KOiK00927.
OMAiFPVDYVT.
OrthoDBiEOG092C2GKC.

Family and domain databases

CDDicd00318. Phosphoglycerate_kinase. 1 hit.
Gene3Di3.40.50.1260. 1 hit.
3.40.50.1270. 1 hit.
HAMAPiMF_00145. Phosphoglyc_kinase. 1 hit.
InterProiIPR001576. Phosphoglycerate_kinase.
IPR015901. Phosphoglycerate_kinase_C.
IPR015911. Phosphoglycerate_kinase_CS.
IPR015824. Phosphoglycerate_kinase_N.
[Graphical view]
PANTHERiPTHR11406. PTHR11406. 1 hit.
PfamiPF00162. PGK. 1 hit.
[Graphical view]
PIRSFiPIRSF000724. Pgk. 1 hit.
PRINTSiPR00477. PHGLYCKINASE.
SUPFAMiSSF53748. SSF53748. 1 hit.
PROSITEiPS00111. PGLYCERATE_KINASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P00560-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLSSKLSVQ DLDLKDKRVF IRVDFNVPLD GKKITSNQRI VAALPTIKYV
60 70 80 90 100
LEHHPRYVVL ASHLGRPNGE RNEKYSLAPV AKELQSLLGK DVTFLNDCVG
110 120 130 140 150
PEVEAAVKAS APGSVILLEN LRYHIEEEGS RKVDGQKVKA SKEDVQKFRH
160 170 180 190 200
ELSSLADVYI NDAFGTAHRA HSSMVGFDLP QRAAGFLLEK ELKYFGKALE
210 220 230 240 250
NPTRPFLAIL GGAKVADKIQ LIDNLLDKVD SIIIGGGMAF TFKKVLENTE
260 270 280 290 300
IGDSIFDKAG AEIVPKLMEK AKAKGVEVVL PVDFIIADAF SADANTKTVT
310 320 330 340 350
DKEGIPAGWQ GLDNGPESRK LFAATVAKAK TIVWNGPPGV FEFEKFAAGT
360 370 380 390 400
KALLDEVVKS SAAGNTVIIG GGDTATVAKK YGVTDKISHV STGGGASLEL
410
LEGKELPGVA FLSEKK
Length:416
Mass (Da):44,738
Last modified:January 23, 2007 - v2
Checksum:i378AB944DB34EFF0
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti185G → S AA sequence (PubMed:7287307).Curated1
Sequence conflicti191E → I AA sequence (PubMed:7287307).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiS19422. KIBYG.
RefSeqiNP_009938.2. NM_001178725.1.

Genome annotation databases

EnsemblFungiiCAA42329; CAA42329; CAA42329.
YCR012W; YCR012W; YCR012W.
GeneIDi850370.
KEGGisce:YCR012W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiS19422. KIBYG.
RefSeqiNP_009938.2. NM_001178725.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1FW8X-ray2.30A74-416[»]
1QPGX-ray2.40A2-416[»]
3PGKX-ray2.50A2-416[»]
ProteinModelPortaliP00560.
SMRiP00560.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi30991. 84 interactors.
DIPiDIP-4152N.
IntActiP00560. 46 interactors.
MINTiMINT-484961.

Chemistry databases

BindingDBiP00560.
ChEMBLiCHEMBL2674.

PTM databases

iPTMnetiP00560.

2D gel databases

COMPLUYEAST-2DPAGEP00560.

Proteomic databases

MaxQBiP00560.
PRIDEiP00560.
TopDownProteomicsiP00560.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiCAA42329; CAA42329; CAA42329.
YCR012W; YCR012W; YCR012W.
GeneIDi850370.
KEGGisce:YCR012W.

Organism-specific databases

EuPathDBiFungiDB:YCR012W.
SGDiS000000605. PGK1.

Phylogenomic databases

GeneTreeiENSGT00390000008820.
HOGENOMiHOG000227107.
InParanoidiP00560.
KOiK00927.
OMAiFPVDYVT.
OrthoDBiEOG092C2GKC.

Enzyme and pathway databases

UniPathwayiUPA00109; UER00185.
BioCyciYEAST:YCR012W-MONOMER.
BRENDAi2.7.2.3. 984.
ReactomeiR-SCE-70171. Glycolysis.
R-SCE-70263. Gluconeogenesis.
SABIO-RKP00560.

Miscellaneous databases

EvolutionaryTraceiP00560.
PROiP00560.

Family and domain databases

CDDicd00318. Phosphoglycerate_kinase. 1 hit.
Gene3Di3.40.50.1260. 1 hit.
3.40.50.1270. 1 hit.
HAMAPiMF_00145. Phosphoglyc_kinase. 1 hit.
InterProiIPR001576. Phosphoglycerate_kinase.
IPR015901. Phosphoglycerate_kinase_C.
IPR015911. Phosphoglycerate_kinase_CS.
IPR015824. Phosphoglycerate_kinase_N.
[Graphical view]
PANTHERiPTHR11406. PTHR11406. 1 hit.
PfamiPF00162. PGK. 1 hit.
[Graphical view]
PIRSFiPIRSF000724. Pgk. 1 hit.
PRINTSiPR00477. PHGLYCKINASE.
SUPFAMiSSF53748. SSF53748. 1 hit.
PROSITEiPS00111. PGLYCERATE_KINASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPGK_YEAST
AccessioniPrimary (citable) accession number: P00560
Secondary accession number(s): D6VR21
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 175 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 314000 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome III
    Yeast (Saccharomyces cerevisiae) chromosome III: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.