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Protein

Phosphoglycerate mutase 1

Gene

GPM1

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

Interconversion of 3- and 2-phosphoglycerate with 2,3-bisphosphoglycerate as the primer of the reaction. Can also Catalyze the reaction of EC 5.4.2.4 (synthase), but with a reduced activity.2 Publications

Miscellaneous

Present with 172000 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

2-phospho-D-glycerate = 3-phospho-D-glycerate.1 Publication

Enzyme regulationi

Inhibited by inositol hexakisphosphate and benzene tri-, tetra- and hexacarboxylates.1 Publication

Kineticsi

kcat is 490 sec(-1) for the mutase reaction, 0.0074 sec(-1) for the synthase reaction and 0.0087 sec(-1) for the phosphatase reaction with 3-phosphoglycerate as substrate.1 Publication
  1. KM=740 µM for 3-phosphoglycerate2 Publications
  2. KM=8.1 µM for 2,3-bisphosphoglycerate (for mutase reaction)2 Publications
  3. KM=2.4 µM for 2,3-bisphosphoglycerate (for phosphatase reaction)2 Publications

    Pathwayi: glycolysis

    This protein is involved in step 3 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
    Active sitei9Tele-phosphohistidine intermediate4 Publications1
    Binding sitei60Substrate1 Publication1
    Active sitei87Proton donor/acceptor1 Publication1
    Binding sitei98Substrate1 Publication1
    Sitei182Transition state stabilizer1 Publication1

    GO - Molecular functioni

    GO - Biological processi

    • gluconeogenesis Source: SGD
    • glycolytic process Source: SGD
    • regulation of pentose-phosphate shunt Source: GO_Central

    Keywordsi

    Molecular functionIsomerase
    Biological processGlycolysis

    Enzyme and pathway databases

    BioCyciMetaCyc:YKL152C-MONOMER.
    YEAST:YKL152C-MONOMER.
    BRENDAi5.4.2.11. 984.
    ReactomeiR-SCE-6798695. Neutrophil degranulation.
    R-SCE-70171. Glycolysis.
    R-SCE-70263. Gluconeogenesis.
    SABIO-RKiP00950.
    UniPathwayiUPA00109; UER00186.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phosphoglycerate mutase 1 (EC:5.4.2.111 Publication)
    Short name:
    PGAM 1
    Alternative name(s):
    BPG-dependent PGAM 1
    MPGM 1
    Phosphoglyceromutase 1
    Gene namesi
    Name:GPM1
    Synonyms:GPM
    Ordered Locus Names:YKL152C
    ORF Names:YKL607
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome XI

    Organism-specific databases

    EuPathDBiFungiDB:YKL152C.
    SGDiS000001635. GPM1.

    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, Membrane, Mitochondrion, Mitochondrion outer membrane

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi169K → P: Causes dissociation of the homotetramer to dimers at low concentrations. 1 Publication1
    Mutagenesisi182H → A: Reduces kcat of the mutase reaction 10000-fold. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00001798392 – 247Phosphoglycerate mutase 1Add BLAST246

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei12PhosphoserineCombined sources1
    Cross-linki31Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Modified residuei49PhosphotyrosineCombined sources1
    Cross-linki57Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Cross-linki71Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Modified residuei116PhosphoserineCombined sources1
    Modified residuei127PhosphoserineCombined sources1
    Modified residuei128PhosphoserineCombined sources1
    Cross-linki139Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Cross-linki175Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Modified residuei185PhosphoserineCombined sources1
    Cross-linki191Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Modified residuei197PhosphoserineCombined sources1

    Keywords - PTMi

    Isopeptide bond, Phosphoprotein, Ubl conjugation

    Proteomic databases

    MaxQBiP00950.
    PRIDEiP00950.
    TopDownProteomicsiP00950.

    2D gel databases

    COMPLUYEAST-2DPAGEiP00950.
    SWISS-2DPAGEiP00950.

    PTM databases

    iPTMnetiP00950.

    Interactioni

    Subunit structurei

    Homotetramer: dimer of dimers.6 Publications

    Protein-protein interaction databases

    BioGridi33985. 65 interactors.
    DIPiDIP-6260N.
    IntActiP00950. 43 interactors.
    MINTiMINT-603921.
    STRINGi4932.YKL152C.

    Structurei

    Secondary structure

    1247
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 8Combined sources6
    Helixi13 – 16Combined sources4
    Helixi30 – 45Combined sources16
    Beta strandi51 – 55Combined sources5
    Helixi59 – 71Combined sources13
    Beta strandi79 – 81Combined sources3
    Helixi83 – 85Combined sources3
    Helixi91 – 93Combined sources3
    Helixi98 – 115Combined sources18
    Beta strandi116 – 118Combined sources3
    Beta strandi126 – 130Combined sources5
    Helixi136 – 138Combined sources3
    Helixi143 – 145Combined sources3
    Helixi152 – 165Combined sources14
    Helixi167 – 172Combined sources6
    Beta strandi177 – 181Combined sources5
    Helixi183 – 194Combined sources12
    Turni198 – 200Combined sources3
    Helixi201 – 203Combined sources3
    Beta strandi208 – 210Combined sources3
    Beta strandi212 – 216Combined sources5
    Turni218 – 220Combined sources3
    Beta strandi222 – 224Combined sources3
    Beta strandi227 – 230Combined sources4
    Turni231 – 233Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1BQ3X-ray2.70A/B/C/D2-247[»]
    1BQ4X-ray2.50A/B/C/D2-247[»]
    1QHFX-ray1.70A/B2-241[»]
    3PGMX-ray2.80A/B2-247[»]
    4PGMX-ray2.30A/B/C/D2-247[»]
    5PGMX-ray2.12A/B/C/D/E/F/G/H2-247[»]
    ProteinModelPortaliP00950.
    SMRiP00950.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00950.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni8 – 15Substrate binding3 Publications8
    Regioni21 – 22Substrate binding2 Publications2
    Regioni87 – 90Substrate binding2 Publications4
    Regioni114 – 115Substrate binding1 Publication2
    Regioni183 – 184Substrate binding2 Publications2

    Compositional bias

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Compositional biasi233 – 242Ala-rich10

    Sequence similaritiesi

    Phylogenomic databases

    GeneTreeiENSGT00390000016700.
    HOGENOMiHOG000221682.
    InParanoidiP00950.
    KOiK01834.
    OMAiRMLPYWY.
    OrthoDBiEOG092C4JJL.

    Family and domain databases

    CDDicd07067. HP_PGM_like. 1 hit.
    Gene3Di3.40.50.1240. 1 hit.
    HAMAPiMF_01039. PGAM_GpmA. 1 hit.
    InterProiView protein in InterPro
    IPR013078. His_Pase_superF_clade-1.
    IPR029033. His_PPase_superfam.
    IPR001345. PG/BPGM_mutase_AS.
    IPR005952. Phosphogly_mut1.
    PANTHERiPTHR11931. PTHR11931. 1 hit.
    PfamiView protein in Pfam
    PF00300. His_Phos_1. 1 hit.
    SMARTiView protein in SMART
    SM00855. PGAM. 1 hit.
    SUPFAMiSSF53254. SSF53254. 1 hit.
    TIGRFAMsiTIGR01258. pgm_1. 1 hit.
    PROSITEiView protein in PROSITE
    PS00175. PG_MUTASE. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    P00950-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MPKLVLVRHG QSEWNEKNLF TGWVDVKLSA KGQQEAARAG ELLKEKKVYP
    60 70 80 90 100
    DVLYTSKLSR AIQTANIALE KADRLWIPVN RSWRLNERHY GDLQGKDKAE
    110 120 130 140 150
    TLKKFGEEKF NTYRRSFDVP PPPIDASSPF SQKGDERYKY VDPNVLPETE
    160 170 180 190 200
    SLALVIDRLL PYWQDVIAKD LLSGKTVMIA AHGNSLRGLV KHLEGISDAD
    210 220 230 240
    IAKLNIPTGI PLVFELDENL KPSKPSYYLD PEAAAAGAAA VANQGKK
    Length:247
    Mass (Da):27,609
    Last modified:January 23, 2007 - v3
    Checksum:i45E1A9CCDBDC104D
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X06408 Genomic DNA. Translation: CAA29698.1.
    X58789 Genomic DNA. Translation: CAA41595.1.
    Z26877 Genomic DNA. Translation: CAA81501.1.
    Z28152 Genomic DNA. Translation: CAA81994.1.
    S57976 Genomic DNA. Translation: AAB26026.1. Different termination.
    BK006944 Genomic DNA. Translation: DAA09011.1.
    PIRiS00358. PMBYY.
    RefSeqiNP_012770.1. NM_001179718.1.

    Genome annotation databases

    EnsemblFungiiYKL152C; YKL152C; YKL152C.
    GeneIDi853705.
    KEGGisce:YKL152C.

    Similar proteinsi

    Entry informationi

    Entry nameiPMG1_YEAST
    AccessioniPrimary (citable) accession number: P00950
    Secondary accession number(s): D6VX45, Q02117
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: January 23, 2007
    Last modified: September 27, 2017
    This is version 197 of the entry and version 3 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

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