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Protein

Phosphoglycerate kinase

Gene

PGK1

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

Functioni

Miscellaneous

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

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 3 (ERR3), Enolase-related protein 1 (ERR1), 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

Keywordsi

Molecular functionKinase, Transferase
Biological processGlycolysis
LigandATP-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

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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
PaxDbiP00560
PRIDEiP00560
TopDownProteomicsiP00560

2D gel databases

COMPLUYEAST-2DPAGEP00560

PTM databases

CarbonylDBiP00560
iPTMnetiP00560

Interactioni

Subunit structurei

Monomer.2 Publications

Protein-protein interaction databases

BioGridi30991, 99 interactors
DIPiDIP-4152N
IntActiP00560, 47 interactors
MINTiP00560
STRINGi4932.YCR012W

Chemistry databases

BindingDBiP00560

Structurei

Secondary structure

1416
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 4Combined sources3
Helixi9 – 11Combined sources3
Beta strandi18 – 22Combined sources5
Beta strandi29 – 35Combined sources7
Helixi38 – 52Combined sources15
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
OMAiDMIFDIG
OrthoDBiEOG092C2GKC

Family and domain databases

CDDicd00318 Phosphoglycerate_kinase, 1 hit
Gene3Di3.40.50.1260, 4 hits
HAMAPiMF_00145 Phosphoglyc_kinase, 1 hit
InterProiView protein in InterPro
IPR001576 Phosphoglycerate_kinase
IPR015911 Phosphoglycerate_kinase_CS
IPR015824 Phosphoglycerate_kinase_N
IPR036043 Phosphoglycerate_kinase_sf
PANTHERiPTHR11406 PTHR11406, 1 hit
PfamiView protein in Pfam
PF00162 PGK, 1 hit
PIRSFiPIRSF000724 Pgk, 1 hit
PRINTSiPR00477 PHGLYCKINASE
SUPFAMiSSF53748 SSF53748, 1 hit
PROSITEiView protein in PROSITE
PS00111 PGLYCERATE_KINASE, 1 hit

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

Similar proteinsi

Entry informationi

Entry nameiPGK_YEAST
AccessioniPrimary (citable) accession number: P00560
Secondary accession number(s): D6VR21
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: May 23, 2018
This is version 188 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

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

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