KPYK_GEOSE
ID KPYK_GEOSE Reviewed; 587 AA.
AC Q02499;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1994, sequence version 2.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Pyruvate kinase {ECO:0000303|PubMed:3711058};
DE Short=PK {ECO:0000305};
DE EC=2.7.1.40 {ECO:0000269|PubMed:15749828, ECO:0000269|PubMed:3711058};
DE AltName: Full=ATP:pyruvate 2-O-phosphotransferase {ECO:0000303|PubMed:3711058};
GN Name=pyk;
OS Geobacillus stearothermophilus (Bacillus stearothermophilus).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus.
OX NCBI_TaxID=1422;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 328-346 AND
RP 393-396.
RC STRAIN=ATCC 29609 / DSM 2027 / NCA 1503 / NCIMB 8924;
RX PubMed=8436141; DOI=10.1111/j.1432-1033.1993.tb17618.x;
RA Sakai H., Ohta T.;
RT "Molecular cloning and nucleotide sequence of the gene for pyruvate kinase
RT of Bacillus stearothermophilus and the production of the enzyme in
RT Escherichia coli. Evidence that the genes for phosphofructokinase and
RT pyruvate kinase constitute an operon.";
RL Eur. J. Biochem. 211:851-859(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-51, AND
RP MUTAGENESIS OF ASP-308 AND TRP-416.
RC STRAIN=ATCC 29609 / DSM 2027 / NCA 1503 / NCIMB 8924;
RX PubMed=1447787; DOI=10.1016/0022-2836(92)90505-e;
RA Walker D., Chia W.N., Muirhead H.;
RT "Key residues in the allosteric transition of Bacillus stearothermophilus
RT pyruvate kinase identified by site-directed mutagenesis.";
RL J. Mol. Biol. 228:265-276(1992).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=3711058; DOI=10.1093/oxfordjournals.jbchem.a135579;
RA Sakai H., Suzuki K., Imahori K.;
RT "Purification and properties of pyruvate kinase from Bacillus
RT stearothermophilus.";
RL J. Biochem. 99:1157-1167(1986).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP MUTAGENESIS OF CYS-9; LYS-221 AND CYS-268.
RX PubMed=15749828; DOI=10.1093/jb/mvi027;
RA Sakai H.;
RT "Mutagenesis of the active site lysine 221 of the pyruvate kinase from
RT Bacillus stearothermophilus.";
RL J. Biochem. 137:141-145(2005).
RN [5]
RP CRYSTALLIZATION.
RX PubMed=16511150; DOI=10.1107/s1744309105021093;
RA Suzuki K., Ito S., Shimizu-Ibuka A., Sakai H.;
RT "Crystallization and preliminary X-ray analysis of pyruvate kinase from
RT Bacillus stearothermophilus.";
RL Acta Crystallogr. F 61:759-761(2005).
RN [6] {ECO:0007744|PDB:2E28}
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF MUTANT SER-9/SER-268, SUBUNIT,
RP DOMAIN, AND MUTAGENESIS OF HIS-425 AND VAL-435.
RX PubMed=18511452; DOI=10.1093/jb/mvn069;
RA Suzuki K., Ito S., Shimizu-Ibuka A., Sakai H.;
RT "Crystal structure of pyruvate kinase from Geobacillus
RT stearothermophilus.";
RL J. Biochem. 144:305-312(2008).
CC -!- FUNCTION: Catalyzes the phosphoryl transfer from phosphoenolpyruvate
CC (PEP) to ADP to form pyruvate and ATP (PubMed:3711058,
CC PubMed:15749828). Has a broad specificity for nucleoside diphosphates
CC and can use ADP, GDP, IDP and UDP (PubMed:3711058).
CC {ECO:0000269|PubMed:15749828, ECO:0000269|PubMed:3711058}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + pyruvate = ADP + H(+) + phosphoenolpyruvate;
CC Xref=Rhea:RHEA:18157, ChEBI:CHEBI:15361, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:58702, ChEBI:CHEBI:456216;
CC EC=2.7.1.40; Evidence={ECO:0000269|PubMed:15749828,
CC ECO:0000269|PubMed:3711058};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:18159;
CC Evidence={ECO:0000269|PubMed:15749828, ECO:0000269|PubMed:3711058};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:3711058};
CC Note=Can also use manganese or cobalt. {ECO:0000269|PubMed:3711058};
CC -!- COFACTOR:
CC Name=K(+); Xref=ChEBI:CHEBI:29103;
CC Evidence={ECO:0000269|PubMed:3711058};
CC Note=Can also use ammonium ions. {ECO:0000269|PubMed:3711058};
CC -!- ACTIVITY REGULATION: Exhibits homotropic positive cooperativity for PEP
CC (PubMed:3711058). Allosterically activated by ribose-5-phosphate, AMP
CC and other nucleoside monophosphates but not by fructose-1,6-
CC bisphosphate (PubMed:3711058). {ECO:0000269|PubMed:3711058}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.186 mM for PEP (in the presence of 0.1 mM ribose-5-phosphate)
CC {ECO:0000269|PubMed:15749828};
CC Note=kcat is 3,204 sec(-1) (in the presence of 0.1 mM ribose-5-
CC phosphate). {ECO:0000269|PubMed:15749828};
CC pH dependence:
CC Optimum pH is 7.2 at 30 degrees Celsius. Optimum pH is 6.8 at 60
CC degrees Celsius. {ECO:0000269|PubMed:3711058};
CC -!- PATHWAY: Carbohydrate degradation; glycolysis; pyruvate from D-
CC glyceraldehyde 3-phosphate: step 5/5. {ECO:0000305}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:18511452,
CC ECO:0000269|PubMed:3711058}.
CC -!- DOMAIN: Contains an extra C-terminal sequence (ECTS), which contains a
CC highly conserved PEP binding motif. {ECO:0000269|PubMed:18511452}.
CC -!- PTM: The N-terminus is blocked. {ECO:0000305|PubMed:3711058}.
CC -!- SIMILARITY: Belongs to the pyruvate kinase family. {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the PEP-utilizing
CC enzyme family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA40994.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; D13095; BAA02406.1; -; Genomic_DNA.
DR EMBL; X57859; CAA40994.1; ALT_FRAME; Genomic_DNA.
DR PIR; S27330; S27330.
DR PIR; S29783; S29783.
DR RefSeq; WP_033014443.1; NZ_RCTK01000004.1.
DR PDB; 2E28; X-ray; 2.40 A; A=1-587.
DR PDBsum; 2E28; -.
DR AlphaFoldDB; Q02499; -.
DR SMR; Q02499; -.
DR PRIDE; Q02499; -.
DR GeneID; 58572631; -.
DR BRENDA; 2.7.1.40; 623.
DR UniPathway; UPA00109; UER00188.
DR EvolutionaryTrace; Q02499; -.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016301; F:kinase activity; IEA:UniProtKB-KW.
DR GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR GO; GO:0030955; F:potassium ion binding; IEA:InterPro.
DR GO; GO:0004743; F:pyruvate kinase activity; IEA:UniProtKB-EC.
DR CDD; cd00288; Pyruvate_Kinase; 1.
DR Gene3D; 2.40.33.10; -; 1.
DR Gene3D; 3.20.20.60; -; 1.
DR Gene3D; 3.40.1380.20; -; 1.
DR InterPro; IPR008279; PEP-util_enz_mobile_dom.
DR InterPro; IPR036637; Phosphohistidine_dom_sf.
DR InterPro; IPR001697; Pyr_Knase.
DR InterPro; IPR015813; Pyrv/PenolPyrv_Kinase-like_dom.
DR InterPro; IPR040442; Pyrv_Kinase-like_dom_sf.
DR InterPro; IPR011037; Pyrv_Knase-like_insert_dom_sf.
DR InterPro; IPR018209; Pyrv_Knase_AS.
DR InterPro; IPR015793; Pyrv_Knase_brl.
DR InterPro; IPR015795; Pyrv_Knase_C.
DR InterPro; IPR036918; Pyrv_Knase_C_sf.
DR InterPro; IPR015806; Pyrv_Knase_insert_dom_sf.
DR PANTHER; PTHR11817; PTHR11817; 1.
DR Pfam; PF00391; PEP-utilizers; 1.
DR Pfam; PF00224; PK; 1.
DR Pfam; PF02887; PK_C; 1.
DR PRINTS; PR01050; PYRUVTKNASE.
DR SUPFAM; SSF50800; SSF50800; 1.
DR SUPFAM; SSF51621; SSF51621; 1.
DR SUPFAM; SSF52009; SSF52009; 1.
DR SUPFAM; SSF52935; SSF52935; 1.
DR TIGRFAMs; TIGR01064; pyruv_kin; 1.
DR PROSITE; PS00110; PYRUVATE_KINASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Allosteric enzyme; ATP-binding; Direct protein sequencing;
KW Glycolysis; Kinase; Magnesium; Metal-binding; Nucleotide-binding;
KW Potassium; Pyruvate; Transferase.
FT CHAIN 1..587
FT /note="Pyruvate kinase"
FT /id="PRO_0000112055"
FT BINDING 33
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P30613"
FT BINDING 35..38
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P14618"
FT BINDING 35
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000250|UniProtKB:P30613"
FT BINDING 37
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000250|UniProtKB:P30613"
FT BINDING 67
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000250|UniProtKB:P30613"
FT BINDING 68
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000250|UniProtKB:P30613"
FT BINDING 74
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P14618"
FT BINDING 157
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P14618"
FT BINDING 221
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P30613"
FT BINDING 223
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P30613"
FT BINDING 246
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P30613"
FT BINDING 247
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P30613"
FT BINDING 247
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P30613"
FT BINDING 279
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P30613"
FT SITE 221
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P00549,
FT ECO:0000305|PubMed:15749828"
FT MUTAGEN 9
FT /note="C->S: Slight decrease in activity; when associated
FT with S-268."
FT /evidence="ECO:0000269|PubMed:15749828"
FT MUTAGEN 221
FT /note="K->C,D,L,R: 10000 to 100000-fold decrease in
FT activity."
FT /evidence="ECO:0000269|PubMed:15749828"
FT MUTAGEN 268
FT /note="C->S: Slight decrease in activity; when associated
FT with S-9."
FT /evidence="ECO:0000269|PubMed:15749828"
FT MUTAGEN 308
FT /note="D->E: Reduced activity; when associated with Y-416."
FT /evidence="ECO:0000269|PubMed:1447787"
FT MUTAGEN 416
FT /note="W->Y: Increased activity."
FT /evidence="ECO:0000269|PubMed:1447787"
FT MUTAGEN 425
FT /note="H->A: Decreases affinity for allosteric activators."
FT /evidence="ECO:0000269|PubMed:18511452"
FT MUTAGEN 435
FT /note="V->E,K,R: Does not affect kinetic properties."
FT /evidence="ECO:0000269|PubMed:18511452"
FT STRAND 5..10
FT /evidence="ECO:0007829|PDB:2E28"
FT TURN 13..15
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 18..27
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 29..35
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 41..57
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 63..67
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 90..96
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 102..108
FT /evidence="ECO:0007829|PDB:2E28"
FT TURN 113..115
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 121..124
FT /evidence="ECO:0007829|PDB:2E28"
FT TURN 125..128
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 129..137
FT /evidence="ECO:0007829|PDB:2E28"
FT TURN 138..141
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 142..146
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 158..160
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 173..185
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 188..194
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 198..210
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 216..222
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 225..229
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 231..237
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 238..244
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 245..251
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 254..256
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 257..271
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 275..282
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 283..286
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 293..305
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 308..313
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 314..317
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 322..337
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 342..350
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 357..371
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 375..380
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 382..384
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 385..392
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 399..405
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 406..411
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 412..414
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 418..422
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 429..443
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 451..456
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 468..473
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 477..480
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 482..486
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 492..495
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 499..505
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 511..515
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 519..521
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 522..525
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 529..535
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 541..549
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 553..555
FT /evidence="ECO:0007829|PDB:2E28"
FT HELIX 560..563
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 569..573
FT /evidence="ECO:0007829|PDB:2E28"
FT TURN 574..577
FT /evidence="ECO:0007829|PDB:2E28"
FT STRAND 578..582
FT /evidence="ECO:0007829|PDB:2E28"
SQ SEQUENCE 587 AA; 62318 MW; 0794BA1A07BE0D5A CRC64;
MKRKTKIVCT IGPASESVDK LVQLMEAGMN VARLNFSHGD HEEHGRRIAN IREAAKRTGR
TVAILLDTKG PEIRTHNMEN GAIELKEGSK LVISMSEVLG TPEKISVTYP SLIDDVSVGA
KILLDDGLIS LEVNAVDKQA GEIVTTVLNG GVLKNKKGVN VPGVKVNLPG ITEKDRADIL
FGIRQGIDFI AASFVRRASD VLEIRELLEA HDALHIQIIA KIENEEGVAN IDEILEAADG
LMVARGDLGV EIPAEEVPLI QKLLIKKCNM LGKPVITATQ MLDSMQRNPR PTRAEASDVA
NAIFDGTDAV MLSGETAAGQ YPVEAVKTMH QIALRTEQAL EHRDILSQRT KESQTTITDA
IGQSVAHTAL NLDVAAIVTP TVSGKTPQMV AKYRPKAPII AVTSNEAVSR RLALVWGVYT
KEAPHVNTTD EMLDVAVDAA VRSGLVKHGD LVVITAGVPV GETGSTNLMK VHVISDLLAK
GQGIGRKSAF GKAVVAKTAE EARQKMVDGG ILVTVSTDAD MMPAIEKAAA IITEEGGLTS
HAAVVGLSLG IPVIVGVENA TTLFKDGQEI TVDGGFGAVY RGHASVL
