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Protein

2,3-bisphosphoglycerate-independent phosphoglycerate mutase

Gene

gpmI

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Essential for rapid growth and for sporulation. Catalyzes the interconversion of 2-phosphoglycerate (2-PGA) and 3-phosphoglycerate (3-PGA).2 Publications

Catalytic activityi

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

Cofactori

Mn2+4 PublicationsNote: Binds 2 manganese ions per subunit.4 Publications

Enzyme regulationi

Could be inhibited during sporulation by acidification of the forespore, thus allowing accumulation of the spore's large depot of 3-phosphoglyceric acid.1 Publication

Kineticsi

  1. KM=4.4 mM for 3-pGA1 Publication

    pH dependencei

    Very sensitive to pH. The enzyme activity rises 25-fold between pH 6 and 8.1 Publication

    Temperature dependencei

    Addition of manganese increases the thermal stability.1 Publication

    Pathwayi: glycolysis

    This protein is involved in step 3 of the subpathway that synthesizes pyruvate from D-glyceraldehyde 3-phosphate.Curated
    Proteins known to be involved in the 5 steps of the subpathway in this organism are:
    1. Glyceraldehyde-3-phosphate dehydrogenase (gap)
    2. Phosphoglycerate kinase (pgk), Phosphoglycerate kinase (pgk), Phosphoglycerate kinase (pgk)
    3. 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (gpmI), 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (gpmI), 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (gpmI)
    4. Enolase (eno), Enolase (eno)
    5. Pyruvate kinase (pyk), Pyruvate kinase (GT94_09925), Pyruvate kinase (AA904_05055)
    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)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi12 – 121Manganese 22 Publications
    Active sitei62 – 621Phosphoserine intermediate3 Publications
    Metal bindingi62 – 621Manganese 22 Publications
    Binding sitei123 – 1231Substrate3 Publications
    Binding sitei185 – 1851Substrate3 Publications
    Binding sitei191 – 1911Substrate2 Publications
    Binding sitei336 – 3361Substrate2 Publications
    Metal bindingi403 – 4031Manganese 13 Publications
    Metal bindingi407 – 4071Manganese 13 Publications
    Metal bindingi444 – 4441Manganese 22 Publications
    Metal bindingi445 – 4451Manganese 22 Publications
    Metal bindingi462 – 4621Manganese 13 Publications

    GO - Molecular functioni

    • 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity Source: UniProtKB
    • manganese ion binding Source: UniProtKB

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Glycolysis, Sporulation

    Keywords - Ligandi

    Manganese, Metal-binding

    Enzyme and pathway databases

    BRENDAi5.4.2.12. 623.
    UniPathwayiUPA00109; UER00186.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2,3-bisphosphoglycerate-independent phosphoglycerate mutase1 Publication (EC:5.4.2.121 Publication)
    Short name:
    23PGA-independent1 Publication
    Short name:
    BPG-independent PGAM1 Publication
    Short name:
    Phosphoglyceromutase1 Publication
    Short name:
    iPGM1 Publication
    Gene namesi
    Name:gpmIUniRule annotation
    Synonyms:pgm
    OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
    Taxonomic identifieri1422 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi12 – 121D → N: Loss of mutase activity. 1 Publication
    Mutagenesisi42 – 421H → N: Decrease in activity. 1 Publication
    Mutagenesisi62 – 621S → A: Loss of mutase activity. 2 Publications
    Mutagenesisi66 – 661H → N: Strong decrease in the mutase activity. 1 Publication
    Mutagenesisi123 – 1231H → N: Strong decrease in the mutase activity. 1 Publication
    Mutagenesisi125 – 1251H → N: Decrease in activity. 1 Publication
    Mutagenesisi128 – 1281H → N: 5-fold decrease in activity. 1 Publication
    Mutagenesisi261 – 2611R → L: Loss of mutase activity. 1 Publication
    Mutagenesisi407 – 4071H → N: Loss of mutase activity. 1 Publication
    Mutagenesisi445 – 4451H → N: 5-fold decrease in the mutase activity. 1 Publication
    Mutagenesisi462 – 4621H → N: Strong decrease in the mutase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved1 Publication
    Chaini2 – 5115102,3-bisphosphoglycerate-independent phosphoglycerate mutasePRO_0000212127Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei36 – 361PhosphotyrosineUniRule annotation

    Keywords - PTMi

    Phosphoprotein

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Structurei

    Secondary structure

    1
    511
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 116Combined sources
    Helixi24 – 274Combined sources
    Helixi31 – 399Combined sources
    Beta strandi42 – 465Combined sources
    Helixi49 – 524Combined sources
    Helixi62 – 7110Combined sources
    Helixi78 – 8710Combined sources
    Helixi91 – 933Combined sources
    Helixi95 – 10713Combined sources
    Beta strandi111 – 1166Combined sources
    Helixi126 – 13813Combined sources
    Beta strandi144 – 1507Combined sources
    Beta strandi152 – 1554Combined sources
    Helixi160 – 17415Combined sources
    Beta strandi178 – 1847Combined sources
    Helixi185 – 1884Combined sources
    Helixi195 – 20713Combined sources
    Beta strandi212 – 2154Combined sources
    Helixi216 – 22510Combined sources
    Helixi230 – 2323Combined sources
    Beta strandi236 – 2394Combined sources
    Beta strandi243 – 2464Combined sources
    Beta strandi254 – 2574Combined sources
    Turni263 – 2653Combined sources
    Helixi266 – 2738Combined sources
    Beta strandi291 – 2966Combined sources
    Beta strandi300 – 3023Combined sources
    Beta strandi304 – 3085Combined sources
    Helixi317 – 3237Combined sources
    Beta strandi328 – 3336Combined sources
    Helixi334 – 3363Combined sources
    Helixi337 – 3404Combined sources
    Turni341 – 3466Combined sources
    Beta strandi355 – 3606Combined sources
    Helixi368 – 3703Combined sources
    Turni372 – 3754Combined sources
    Helixi376 – 38813Combined sources
    Beta strandi393 – 3997Combined sources
    Helixi401 – 4066Combined sources
    Turni407 – 4093Combined sources
    Helixi411 – 43424Combined sources
    Beta strandi438 – 4425Combined sources
    Beta strandi444 – 4474Combined sources
    Beta strandi467 – 4715Combined sources
    Beta strandi480 – 4834Combined sources
    Helixi484 – 4863Combined sources
    Helixi487 – 4959Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EJJX-ray1.90A1-511[»]
    1EQJX-ray1.70A1-511[»]
    1O98X-ray1.40A1-511[»]
    1O99X-ray2.65A1-511[»]
    ProteinModelPortaliQ9X519.
    SMRiQ9X519. Positions 2-510.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9X519.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni153 – 1542Substrate binding3 Publications
    Regioni261 – 2644Substrate binding3 Publications

    Sequence similaritiesi

    Phylogenomic databases

    KOiK15633.

    Family and domain databases

    Gene3Di3.40.1450.10. 1 hit.
    3.40.720.10. 2 hits.
    HAMAPiMF_01038. GpmI.
    InterProiIPR017849. Alkaline_Pase-like_a/b/a.
    IPR017850. Alkaline_phosphatase_core.
    IPR011258. BPG-indep_PGM_N.
    IPR006124. Metalloenzyme.
    IPR005995. Pgm_bpd_ind.
    [Graphical view]
    PfamiPF06415. iPGM_N. 1 hit.
    PF01676. Metalloenzyme. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001492. IPGAM. 1 hit.
    SUPFAMiSSF53649. SSF53649. 2 hits.
    SSF64158. SSF64158. 1 hit.
    TIGRFAMsiTIGR01307. pgm_bpd_ind. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    Q9X519-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSKKPVALII LDGFALRDET YGNAVAQANK PNFDRYWNEY PHTTLKACGE
    60 70 80 90 100
    AVGLPEGQMG NSEVGHLNIG AGRIVYQSLT RINIAIREGE FDRNETFLAA
    110 120 130 140 150
    MNHVKQHGTS LHLFGLLSDG GVHSHIHHLY ALLRLAAKEG VKRVYIHGFL
    160 170 180 190 200
    DGRDVGPQTA PQYIKELQEK IKEYGVGEIA TLSGRYYSMD RDKRWDRVEK
    210 220 230 240 250
    AYRAMVYGEG PTYRDPLECI EDSYKHGIYD EFVLPSVIVR EDGRPVATIQ
    260 270 280 290 300
    DNDAIIFYNF RPDRAIQISN TFTNEDFREF DRGPKHPKHL FFVCLTHFSE
    310 320 330 340 350
    TVKGYVAFKP TNLDNTIGEV LSQHGLRQLR IAETEKYPHV TFFMSGGREE
    360 370 380 390 400
    KFPGEDRILI NSPKVPTYDL KPEMSAYEVT DALLKEIEAD KYDAIILNYA
    410 420 430 440 450
    NPDMVGHSGK LEPTIKAVEA VDECLGKVVD AILAKGGIAI ITADHGNADE
    460 470 480 490 500
    VLTPDGKPQT AHTTNPVPVI VTKKGIKLRD GGILGDLAPT MLDLLGLPQP
    510
    KEMTGKSLIV K
    Length:511
    Mass (Da):57,003
    Last modified:January 23, 2007 - v3
    Checksum:i45E4F5CEE457A04B
    GO

    Mass spectrometryi

    Molecular mass is 56877 Da from positions 2 - 511. Determined by MALDI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF120091 Genomic DNA. Translation: AAD26328.1.
    PIRiT46865.

    Genome annotation databases

    KEGGiag:AAD26328.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF120091 Genomic DNA. Translation: AAD26328.1.
    PIRiT46865.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EJJX-ray1.90A1-511[»]
    1EQJX-ray1.70A1-511[»]
    1O98X-ray1.40A1-511[»]
    1O99X-ray2.65A1-511[»]
    ProteinModelPortaliQ9X519.
    SMRiQ9X519. Positions 2-510.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:AAD26328.

    Phylogenomic databases

    KOiK15633.

    Enzyme and pathway databases

    UniPathwayiUPA00109; UER00186.
    BRENDAi5.4.2.12. 623.

    Miscellaneous databases

    EvolutionaryTraceiQ9X519.

    Family and domain databases

    Gene3Di3.40.1450.10. 1 hit.
    3.40.720.10. 2 hits.
    HAMAPiMF_01038. GpmI.
    InterProiIPR017849. Alkaline_Pase-like_a/b/a.
    IPR017850. Alkaline_phosphatase_core.
    IPR011258. BPG-indep_PGM_N.
    IPR006124. Metalloenzyme.
    IPR005995. Pgm_bpd_ind.
    [Graphical view]
    PfamiPF06415. iPGM_N. 1 hit.
    PF01676. Metalloenzyme. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001492. IPGAM. 1 hit.
    SUPFAMiSSF53649. SSF53649. 2 hits.
    SSF64158. SSF64158. 1 hit.
    TIGRFAMsiTIGR01307. pgm_bpd_ind. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "Structural studies on a 2,3-diphosphoglycerate independent phosphoglycerate mutase from Bacillus stearothermophilus."
      Chander M., Setlow P., Lamani E., Jedrzejas M.J.
      J. Struct. Biol. 126:156-165(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-8, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, MASS SPECTROMETRY, CRYSTALLIZATION, SUBUNIT.
    2. "Structure and mechanism of action of a novel phosphoglycerate mutase from Bacillus stearothermophilus."
      Jedrzejas M.J., Chander M., Setlow P., Krishnasamy G.
      EMBO J. 19:1419-1431(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND MANGANESE, FUNCTION, MUTAGENESIS OF ASP-12; HIS-42; SER-62; HIS-66; HIS-123; HIS-125; HIS-128; ARG-261; HIS-407 AND HIS-445, COFACTOR, ACTIVE SITE, REACTION MECHANISM.
    3. "Mechanism of catalysis of the cofactor-independent phosphoglycerate mutase from Bacillus stearothermophilus. Crystal structure of the complex with 2-phosphoglycerate."
      Jedrzejas M.J., Chander M., Setlow P., Krishnasamy G.
      J. Biol. Chem. 275:23146-23153(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND MANGANESE, COFACTOR.
    4. "Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling."
      Rigden D.J., Lamani E., Mello L.V., Littlejohn J.E., Jedrzejas M.J.
      J. Mol. Biol. 328:909-920(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS) OF WILD-TYPE AND MUTANT ALA-62 IN COMPLEX WITH SUBSTRATE AND MANGANESE, MUTAGENESIS OF SER-62, COFACTOR, ACTIVE SITE.

    Entry informationi

    Entry nameiGPMI_GEOSE
    AccessioniPrimary (citable) accession number: Q9X519
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 10, 2003
    Last sequence update: January 23, 2007
    Last modified: December 9, 2015
    This is version 95 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The pH sensitivity is physiologically relevant, since it allows for the regulation of iPGM activity during different parts of the developmental cycle.1 Publication

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    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

    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.