GPMI_GEOSE
ID GPMI_GEOSE Reviewed; 511 AA.
AC Q9X519;
DT 10-JAN-2003, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=2,3-bisphosphoglycerate-independent phosphoglycerate mutase {ECO:0000303|PubMed:10388626};
DE Short=23PGA-independent {ECO:0000303|PubMed:10388626};
DE Short=BPG-independent PGAM {ECO:0000303|PubMed:10388626};
DE Short=Phosphoglyceromutase {ECO:0000303|PubMed:10388626};
DE Short=iPGM {ECO:0000303|PubMed:10388626};
DE EC=5.4.2.12 {ECO:0000269|PubMed:10388626};
GN Name=gpmI {ECO:0000255|HAMAP-Rule:MF_01038}; Synonyms=pgm;
OS Geobacillus stearothermophilus (Bacillus stearothermophilus).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus.
OX NCBI_TaxID=1422;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-8, FUNCTION,
RP CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, MASS
RP SPECTROMETRY, CRYSTALLIZATION, AND SUBUNIT.
RX PubMed=10388626; DOI=10.1006/jsbi.1999.4112;
RA Chander M., Setlow P., Lamani E., Jedrzejas M.J.;
RT "Structural studies on a 2,3-diphosphoglycerate independent
RT phosphoglycerate mutase from Bacillus stearothermophilus.";
RL J. Struct. Biol. 126:156-165(1999).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND
RP MANGANESE, FUNCTION, MUTAGENESIS OF ASP-12; HIS-42; SER-62; HIS-66;
RP HIS-123; HIS-125; HIS-128; ARG-261; HIS-407 AND HIS-445, COFACTOR, ACTIVE
RP SITE, AND REACTION MECHANISM.
RX PubMed=10747010; DOI=10.1093/emboj/19.7.1419;
RA Jedrzejas M.J., Chander M., Setlow P., Krishnasamy G.;
RT "Structure and mechanism of action of a novel phosphoglycerate mutase from
RT Bacillus stearothermophilus.";
RL EMBO J. 19:1419-1431(2000).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND
RP MANGANESE, AND COFACTOR.
RX PubMed=10764795; DOI=10.1074/jbc.m002544200;
RA Jedrzejas M.J., Chander M., Setlow P., Krishnasamy G.;
RT "Mechanism of catalysis of the cofactor-independent phosphoglycerate mutase
RT from Bacillus stearothermophilus. Crystal structure of the complex with 2-
RT phosphoglycerate.";
RL J. Biol. Chem. 275:23146-23153(2000).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS) OF WILD-TYPE AND MUTANT ALA-62 IN
RP COMPLEX WITH SUBSTRATE AND MANGANESE, MUTAGENESIS OF SER-62, COFACTOR, AND
RP ACTIVE SITE.
RX PubMed=12729763; DOI=10.1016/s0022-2836(03)00350-4;
RA Rigden D.J., Lamani E., Mello L.V., Littlejohn J.E., Jedrzejas M.J.;
RT "Insights into the catalytic mechanism of cofactor-independent
RT phosphoglycerate mutase from X-ray crystallography, simulated dynamics and
RT molecular modeling.";
RL J. Mol. Biol. 328:909-920(2003).
CC -!- FUNCTION: Essential for rapid growth and for sporulation. Catalyzes the
CC interconversion of 2-phosphoglycerate (2-PGA) and 3-phosphoglycerate
CC (3-PGA). {ECO:0000269|PubMed:10388626, ECO:0000269|PubMed:10747010}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate;
CC Xref=Rhea:RHEA:15901, ChEBI:CHEBI:58272, ChEBI:CHEBI:58289;
CC EC=5.4.2.12; Evidence={ECO:0000269|PubMed:10388626};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:10388626, ECO:0000269|PubMed:10747010,
CC ECO:0000269|PubMed:10764795, ECO:0000269|PubMed:12729763};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000269|PubMed:10388626,
CC ECO:0000269|PubMed:10747010, ECO:0000269|PubMed:10764795,
CC ECO:0000269|PubMed:12729763};
CC -!- ACTIVITY REGULATION: Could be inhibited during sporulation by
CC acidification of the forespore, thus allowing accumulation of the
CC spore's large depot of 3-phosphoglyceric acid.
CC {ECO:0000305|PubMed:10388626}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=4.4 mM for 3-pGA {ECO:0000269|PubMed:10388626};
CC pH dependence:
CC Very sensitive to pH. The enzyme activity rises 25-fold between pH 6
CC and 8. {ECO:0000269|PubMed:10388626};
CC Temperature dependence:
CC Addition of manganese increases the thermal stability.
CC {ECO:0000269|PubMed:10388626};
CC -!- PATHWAY: Carbohydrate degradation; glycolysis; pyruvate from D-
CC glyceraldehyde 3-phosphate: step 3/5. {ECO:0000305}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:10388626}.
CC -!- MASS SPECTROMETRY: Mass=56877; Method=MALDI;
CC Evidence={ECO:0000269|PubMed:10388626};
CC -!- MISCELLANEOUS: The pH sensitivity is physiologically relevant, since it
CC allows for the regulation of iPGM activity during different parts of
CC the developmental cycle. {ECO:0000305|PubMed:10764795}.
CC -!- SIMILARITY: Belongs to the BPG-independent phosphoglycerate mutase
CC family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AF120091; AAD26328.1; -; Genomic_DNA.
DR PIR; T46865; T46865.
DR RefSeq; WP_033015095.1; NZ_RCTH01000020.1.
DR PDB; 1EJJ; X-ray; 1.90 A; A=1-511.
DR PDB; 1EQJ; X-ray; 1.70 A; A=1-511.
DR PDB; 1O98; X-ray; 1.40 A; A=1-511.
DR PDB; 1O99; X-ray; 2.65 A; A=1-511.
DR PDBsum; 1EJJ; -.
DR PDBsum; 1EQJ; -.
DR PDBsum; 1O98; -.
DR PDBsum; 1O99; -.
DR AlphaFoldDB; Q9X519; -.
DR SMR; Q9X519; -.
DR DrugBank; DB01709; 2-phospho-D-glyceric acid.
DR DrugBank; DB04510; 3-phospho-D-glyceric acid.
DR KEGG; ag:AAD26328; -.
DR BRENDA; 5.4.2.12; 623.
DR SABIO-RK; Q9X519; -.
DR UniPathway; UPA00109; UER00186.
DR EvolutionaryTrace; Q9X519; -.
DR GO; GO:0005737; C:cytoplasm; IEA:InterPro.
DR GO; GO:0046537; F:2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity; IDA:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
DR GO; GO:0006007; P:glucose catabolic process; IEA:InterPro.
DR GO; GO:0006096; P:glycolytic process; IEA:UniProtKB-UniRule.
DR GO; GO:0043937; P:regulation of sporulation; IDA:UniProtKB.
DR GO; GO:0030435; P:sporulation resulting in formation of a cellular spore; IEA:UniProtKB-KW.
DR CDD; cd16010; iPGM; 1.
DR Gene3D; 3.40.1450.10; -; 1.
DR Gene3D; 3.40.720.10; -; 1.
DR HAMAP; MF_01038; GpmI; 1.
DR InterPro; IPR017850; Alkaline_phosphatase_core_sf.
DR InterPro; IPR011258; BPG-indep_PGM_N.
DR InterPro; IPR006124; Metalloenzyme.
DR InterPro; IPR036646; PGAM_B_sf.
DR InterPro; IPR005995; Pgm_bpd_ind.
DR PANTHER; PTHR31637; PTHR31637; 1.
DR Pfam; PF06415; iPGM_N; 1.
DR Pfam; PF01676; Metalloenzyme; 1.
DR PIRSF; PIRSF001492; IPGAM; 1.
DR SUPFAM; SSF53649; SSF53649; 1.
DR SUPFAM; SSF64158; SSF64158; 1.
DR TIGRFAMs; TIGR01307; pgm_bpd_ind; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Glycolysis; Isomerase; Manganese;
KW Metal-binding; Phosphoprotein; Sporulation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:10388626"
FT CHAIN 2..511
FT /note="2,3-bisphosphoglycerate-independent phosphoglycerate
FT mutase"
FT /id="PRO_0000212127"
FT ACT_SITE 62
FT /note="Phosphoserine intermediate"
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:10764795, ECO:0000269|PubMed:12729763"
FT BINDING 12
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:10764795"
FT BINDING 62
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:10764795"
FT BINDING 123
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:10764795, ECO:0000269|PubMed:12729763"
FT BINDING 153..154
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:10764795, ECO:0000269|PubMed:12729763"
FT BINDING 185
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:10764795, ECO:0000269|PubMed:12729763"
FT BINDING 191
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:10764795"
FT BINDING 261..264
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:10764795, ECO:0000269|PubMed:12729763"
FT BINDING 336
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:12729763"
FT BINDING 403
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:10764795, ECO:0000269|PubMed:12729763"
FT BINDING 407
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:10764795, ECO:0000269|PubMed:12729763"
FT BINDING 444
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:10764795"
FT BINDING 445
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:10764795"
FT BINDING 462
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:10764795, ECO:0000269|PubMed:12729763"
FT MOD_RES 36
FT /note="Phosphotyrosine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01038"
FT MUTAGEN 12
FT /note="D->N: Loss of mutase activity."
FT /evidence="ECO:0000269|PubMed:10747010"
FT MUTAGEN 42
FT /note="H->N: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:10747010"
FT MUTAGEN 62
FT /note="S->A: Loss of mutase activity."
FT /evidence="ECO:0000269|PubMed:10747010,
FT ECO:0000269|PubMed:12729763"
FT MUTAGEN 66
FT /note="H->N: Strong decrease in the mutase activity."
FT /evidence="ECO:0000269|PubMed:10747010"
FT MUTAGEN 123
FT /note="H->N: Strong decrease in the mutase activity."
FT /evidence="ECO:0000269|PubMed:10747010"
FT MUTAGEN 125
FT /note="H->N: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:10747010"
FT MUTAGEN 128
FT /note="H->N: 5-fold decrease in activity."
FT /evidence="ECO:0000269|PubMed:10747010"
FT MUTAGEN 261
FT /note="R->L: Loss of mutase activity."
FT /evidence="ECO:0000269|PubMed:10747010"
FT MUTAGEN 407
FT /note="H->N: Loss of mutase activity."
FT /evidence="ECO:0000269|PubMed:10747010"
FT MUTAGEN 445
FT /note="H->N: 5-fold decrease in the mutase activity."
FT /evidence="ECO:0000269|PubMed:10747010"
FT MUTAGEN 462
FT /note="H->N: Strong decrease in the mutase activity."
FT /evidence="ECO:0000269|PubMed:10747010"
FT STRAND 6..11
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 24..27
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 31..39
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 42..46
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 49..52
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 62..71
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 78..87
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 91..93
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 95..107
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 111..116
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 126..138
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 144..150
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 152..155
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 160..174
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 178..184
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 185..188
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 195..207
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 212..215
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 216..225
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 230..232
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 236..239
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 243..246
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 254..257
FT /evidence="ECO:0007829|PDB:1O98"
FT TURN 263..265
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 266..273
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 291..296
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 300..302
FT /evidence="ECO:0007829|PDB:1EJJ"
FT STRAND 304..308
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 317..323
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 328..333
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 334..336
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 337..340
FT /evidence="ECO:0007829|PDB:1O98"
FT TURN 341..346
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 355..360
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 368..370
FT /evidence="ECO:0007829|PDB:1O98"
FT TURN 372..375
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 376..388
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 393..399
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 401..406
FT /evidence="ECO:0007829|PDB:1O98"
FT TURN 407..409
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 411..434
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 438..442
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 444..447
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 467..471
FT /evidence="ECO:0007829|PDB:1O98"
FT STRAND 480..483
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 484..486
FT /evidence="ECO:0007829|PDB:1O98"
FT HELIX 487..495
FT /evidence="ECO:0007829|PDB:1O98"
SQ SEQUENCE 511 AA; 57003 MW; 45E4F5CEE457A04B CRC64;
MSKKPVALII LDGFALRDET YGNAVAQANK PNFDRYWNEY PHTTLKACGE AVGLPEGQMG
NSEVGHLNIG AGRIVYQSLT RINIAIREGE FDRNETFLAA MNHVKQHGTS LHLFGLLSDG
GVHSHIHHLY ALLRLAAKEG VKRVYIHGFL DGRDVGPQTA PQYIKELQEK IKEYGVGEIA
TLSGRYYSMD RDKRWDRVEK AYRAMVYGEG PTYRDPLECI EDSYKHGIYD EFVLPSVIVR
EDGRPVATIQ DNDAIIFYNF RPDRAIQISN TFTNEDFREF DRGPKHPKHL FFVCLTHFSE
TVKGYVAFKP TNLDNTIGEV LSQHGLRQLR IAETEKYPHV TFFMSGGREE KFPGEDRILI
NSPKVPTYDL KPEMSAYEVT DALLKEIEAD KYDAIILNYA NPDMVGHSGK LEPTIKAVEA
VDECLGKVVD AILAKGGIAI ITADHGNADE VLTPDGKPQT AHTTNPVPVI VTKKGIKLRD
GGILGDLAPT MLDLLGLPQP KEMTGKSLIV K
