IPK_METJA
ID IPK_METJA Reviewed; 260 AA.
AC Q60352;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=Isopentenyl phosphate kinase;
DE Short=IPK;
DE EC=2.7.4.26;
GN OrderedLocusNames=MJ0044;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP IDENTIFICATION, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND CATALYTIC
RP ACTIVITY.
RX PubMed=16621811; DOI=10.1128/jb.188.9.3192-3198.2006;
RA Grochowski L.L., Xu H., White R.H.;
RT "Methanocaldococcus jannaschii uses a modified mevalonate pathway for
RT biosynthesis of isopentenyl diphosphate.";
RL J. Bacteriol. 188:3192-3198(2006).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEXES WITH ISOPENTENYL
RP PHOSPHATE; ISOPENTENYL DIPHOSPHATE AND SULFATE, CATALYTIC ACTIVITY,
RP FUNCTION, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF
RP HIS-60; PHE-83; ILE-86 AND ILE-156.
RX PubMed=20392112; DOI=10.1021/cb1000313;
RA Dellas N., Noel J.P.;
RT "Mutation of archaeal isopentenyl phosphate kinase highlights mechanism and
RT guides phosphorylation of additional isoprenoid monophosphates.";
RL ACS Chem. Biol. 5:589-601(2010).
CC -!- FUNCTION: Catalyzes the formation of isopentenyl diphosphate (IPP), the
CC building block of all isoprenoids. Has no activity with farnesyl
CC phosphate. {ECO:0000269|PubMed:16621811, ECO:0000269|PubMed:20392112}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + isopentenyl phosphate = ADP + isopentenyl diphosphate;
CC Xref=Rhea:RHEA:33963, ChEBI:CHEBI:30616, ChEBI:CHEBI:65078,
CC ChEBI:CHEBI:128769, ChEBI:CHEBI:456216; EC=2.7.4.26;
CC Evidence={ECO:0000269|PubMed:16621811, ECO:0000269|PubMed:20392112};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=4.3 uM for isopentenyl phosphate {ECO:0000269|PubMed:16621811,
CC ECO:0000269|PubMed:20392112};
CC KM=198 uM for ATP {ECO:0000269|PubMed:16621811,
CC ECO:0000269|PubMed:20392112};
CC pH dependence:
CC Optimum pH is 7-9. {ECO:0000269|PubMed:16621811,
CC ECO:0000269|PubMed:20392112};
CC Temperature dependence:
CC Retains 38% activity when incubated at 100 degrees Celsius for 10
CC minutes. {ECO:0000269|PubMed:16621811, ECO:0000269|PubMed:20392112};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:20392112}.
CC -!- SIMILARITY: Belongs to the isopentenyl phosphate kinase family.
CC {ECO:0000305}.
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DR EMBL; L77117; AAB98024.1; -; Genomic_DNA.
DR PIR; D64305; D64305.
DR RefSeq; WP_010869535.1; NC_000909.1.
DR PDB; 3K4O; X-ray; 2.05 A; A/B=1-260.
DR PDB; 3K4Y; X-ray; 2.54 A; A/B=1-260.
DR PDB; 3K52; X-ray; 2.70 A; A/B=1-260.
DR PDB; 3K56; X-ray; 2.34 A; A/B=1-260.
DR PDBsum; 3K4O; -.
DR PDBsum; 3K4Y; -.
DR PDBsum; 3K52; -.
DR PDBsum; 3K56; -.
DR AlphaFoldDB; Q60352; -.
DR SMR; Q60352; -.
DR STRING; 243232.MJ_0044; -.
DR EnsemblBacteria; AAB98024; AAB98024; MJ_0044.
DR GeneID; 1450882; -.
DR KEGG; mja:MJ_0044; -.
DR eggNOG; arCOG00860; Archaea.
DR HOGENOM; CLU_070213_0_0_2; -.
DR InParanoid; Q60352; -.
DR OMA; HHNASEH; -.
DR OrthoDB; 96284at2157; -.
DR PhylomeDB; Q60352; -.
DR BioCyc; MetaCyc:MON-14619; -.
DR BRENDA; 2.7.4.26; 3260.
DR EvolutionaryTrace; Q60352; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0102043; F:isopentenyl phosphate kinase activity; IEA:UniProtKB-EC.
DR GO; GO:0016301; F:kinase activity; IEA:UniProtKB-KW.
DR GO; GO:0008299; P:isoprenoid biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR CDD; cd04241; AAK_FomA-like; 1.
DR Gene3D; 3.40.1160.10; -; 1.
DR InterPro; IPR036393; AceGlu_kinase-like_sf.
DR InterPro; IPR001048; Asp/Glu/Uridylate_kinase.
DR InterPro; IPR024192; Fosfomycin_R_FomA-type.
DR InterPro; IPR001057; Glu/AcGlu_kinase.
DR PANTHER; PTHR43654:SF1; PTHR43654:SF1; 1.
DR Pfam; PF00696; AA_kinase; 1.
DR PIRSF; PIRSF016496; Kin_FomA; 1.
DR PRINTS; PR00474; GLU5KINASE.
DR SUPFAM; SSF53633; SSF53633; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Isoprene biosynthesis; Kinase;
KW Nucleotide-binding; Reference proteome; Transferase.
FT CHAIN 1..260
FT /note="Isopentenyl phosphate kinase"
FT /id="PRO_0000106666"
FT BINDING 6..10
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305"
FT BINDING 55
FT /ligand="substrate"
FT BINDING 56
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 60
FT /ligand="substrate"
FT BINDING 159
FT /ligand="substrate"
FT BINDING 180
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 217
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 221
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305"
FT SITE 15
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250"
FT MUTAGEN 60
FT /note="H->A,N: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:20392112"
FT MUTAGEN 60
FT /note="H->Q: Nearly abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:20392112"
FT MUTAGEN 83
FT /note="F->A: Confers activity with farnesyl phosphate; when
FT associated with A-86 and A-156. Confers low activity with
FT farnesyl phosphate."
FT /evidence="ECO:0000269|PubMed:20392112"
FT MUTAGEN 86
FT /note="I->A: Confers activity with farnesyl phosphate; when
FT associated with A-83 and A-156."
FT /evidence="ECO:0000269|PubMed:20392112"
FT MUTAGEN 86
FT /note="I->G: Confers low activity with farnesyl phosphate."
FT /evidence="ECO:0000269|PubMed:20392112"
FT MUTAGEN 156
FT /note="I->A: Confers activity with farnesyl phosphate; when
FT associated with A-83 and A-86."
FT /evidence="ECO:0000269|PubMed:20392112"
FT MUTAGEN 156
FT /note="I->G: Confers low activity with farnesyl phosphate."
FT /evidence="ECO:0000269|PubMed:20392112"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:3K4O"
FT HELIX 9..12
FT /evidence="ECO:0007829|PDB:3K56"
FT HELIX 23..42
FT /evidence="ECO:0007829|PDB:3K4O"
FT STRAND 48..53
FT /evidence="ECO:0007829|PDB:3K4O"
FT HELIX 56..63
FT /evidence="ECO:0007829|PDB:3K4O"
FT HELIX 64..66
FT /evidence="ECO:0007829|PDB:3K4O"
FT STRAND 67..69
FT /evidence="ECO:0007829|PDB:3K4O"
FT STRAND 71..76
FT /evidence="ECO:0007829|PDB:3K4O"
FT HELIX 79..102
FT /evidence="ECO:0007829|PDB:3K4O"
FT TURN 103..105
FT /evidence="ECO:0007829|PDB:3K4O"
FT STRAND 108..111
FT /evidence="ECO:0007829|PDB:3K4O"
FT HELIX 113..115
FT /evidence="ECO:0007829|PDB:3K4O"
FT STRAND 118..122
FT /evidence="ECO:0007829|PDB:3K4O"
FT HELIX 128..135
FT /evidence="ECO:0007829|PDB:3K4O"
FT STRAND 139..143
FT /evidence="ECO:0007829|PDB:3K4O"
FT STRAND 145..152
FT /evidence="ECO:0007829|PDB:3K4O"
FT STRAND 154..157
FT /evidence="ECO:0007829|PDB:3K4O"
FT HELIX 159..170
FT /evidence="ECO:0007829|PDB:3K4O"
FT STRAND 173..190
FT /evidence="ECO:0007829|PDB:3K4O"
FT STRAND 192..194
FT /evidence="ECO:0007829|PDB:3K4O"
FT TURN 196..198
FT /evidence="ECO:0007829|PDB:3K4O"
FT HELIX 199..207
FT /evidence="ECO:0007829|PDB:3K4O"
FT STRAND 208..210
FT /evidence="ECO:0007829|PDB:3K4Y"
FT HELIX 217..227
FT /evidence="ECO:0007829|PDB:3K4O"
FT STRAND 231..236
FT /evidence="ECO:0007829|PDB:3K4O"
FT HELIX 242..247
FT /evidence="ECO:0007829|PDB:3K4O"
FT STRAND 253..257
FT /evidence="ECO:0007829|PDB:3K4O"
SQ SEQUENCE 260 AA; 29472 MW; 833C2BFF020E3F07 CRC64;
MLTILKLGGS ILSDKNVPYS IKWDNLERIA MEIKNALDYY KNQNKEIKLI LVHGGGAFGH
PVAKKYLKIE DGKKIFINME KGFWEIQRAM RRFNNIIIDT LQSYDIPAVS IQPSSFVVFG
DKLIFDTSAI KEMLKRNLVP VIHGDIVIDD KNGYRIISGD DIVPYLANEL KADLILYATD
VDGVLIDNKP IKRIDKNNIY KILNYLSGSN SIDVTGGMKY KIDMIRKNKC RGFVFNGNKA
NNIYKALLGE VEGTEIDFSE
