GLPK_THEKO
ID GLPK_THEKO Reviewed; 497 AA.
AC O93623; Q5JGZ4;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 29-MAR-2005, sequence version 2.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=Glycerol kinase {ECO:0000255|HAMAP-Rule:MF_00186};
DE EC=2.7.1.30 {ECO:0000255|HAMAP-Rule:MF_00186};
DE AltName: Full=ATP:glycerol 3-phosphotransferase {ECO:0000255|HAMAP-Rule:MF_00186};
DE AltName: Full=Glycerokinase {ECO:0000255|HAMAP-Rule:MF_00186};
DE Short=GK {ECO:0000255|HAMAP-Rule:MF_00186};
GN Name=glpK {ECO:0000255|HAMAP-Rule:MF_00186}; OrderedLocusNames=TK1396;
OS Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS (Pyrococcus kodakaraensis (strain KOD1)).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Thermococcus.
OX NCBI_TaxID=69014;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-10, FUNCTION,
RP CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY,
RP AND SUBUNIT.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=9930671; DOI=10.1093/protein/11.12.1219;
RA Koga Y., Morikawa M., Haruki M., Nakamura H., Imanaka T., Kanaya S.;
RT "Thermostable glycerol kinase from a hyperthermophilic archaeon: gene
RT cloning and characterization of the recombinant enzyme.";
RL Protein Eng. 11:1219-1227(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=15710748; DOI=10.1101/gr.3003105;
RA Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL Genome Res. 15:352-363(2005).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS), THERMOSTABILITY, AND SUBUNIT.
RX PubMed=18422647; DOI=10.1111/j.1742-4658.2008.06410.x;
RA Koga Y., Katsumi R., You D.J., Matsumura H., Takano K., Kanaya S.;
RT "Crystal structure of highly thermostable glycerol kinase from a
RT hyperthermophilic archaeon in a dimeric form.";
RL FEBS J. 275:2632-2643(2008).
CC -!- FUNCTION: Key enzyme in the regulation of glycerol uptake and
CC metabolism. Catalyzes the phosphorylation of glycerol to yield sn-
CC glycerol 3-phosphate. Can utilize other nucleoside triphosphates (GTP,
CC CTP, UTP AND ITP) as a phosphoryl donor. {ECO:0000255|HAMAP-
CC Rule:MF_00186, ECO:0000269|PubMed:9930671}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + glycerol = ADP + H(+) + sn-glycerol 3-phosphate;
CC Xref=Rhea:RHEA:21644, ChEBI:CHEBI:15378, ChEBI:CHEBI:17754,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:57597, ChEBI:CHEBI:456216;
CC EC=2.7.1.30; Evidence={ECO:0000255|HAMAP-Rule:MF_00186,
CC ECO:0000269|PubMed:9930671};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=15.4 uM for ATP (at pH 7.5 and 80 degrees Celsius)
CC {ECO:0000269|PubMed:9930671};
CC KM=111 uM for glycerol (at pH 7.5 and 80 degrees Celsius)
CC {ECO:0000269|PubMed:9930671};
CC Note=kcat is 940 sec(-1) for glycerol (at pH 7.5 and 80 degrees
CC Celsius).;
CC pH dependence:
CC Optimum pH is 8.0. It is highly thermosatble.
CC {ECO:0000269|PubMed:9930671};
CC Temperature dependence:
CC Optimum temperature is 80 degrees Celsius.
CC {ECO:0000269|PubMed:9930671};
CC -!- PATHWAY: Polyol metabolism; glycerol degradation via glycerol kinase
CC pathway; sn-glycerol 3-phosphate from glycerol: step 1/1.
CC {ECO:0000255|HAMAP-Rule:MF_00186}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:18422647,
CC ECO:0000269|PubMed:9930671}.
CC -!- MISCELLANEOUS: It is not sensitive to fructose-1,6-bisphosphate (FBP).
CC {ECO:0000305|PubMed:9930671}.
CC -!- SIMILARITY: Belongs to the FGGY kinase family. {ECO:0000255|HAMAP-
CC Rule:MF_00186}.
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DR EMBL; AB012099; BAA34909.1; -; Genomic_DNA.
DR EMBL; AP006878; BAD85585.1; -; Genomic_DNA.
DR PIR; T43888; T43888.
DR RefSeq; WP_011250347.1; NC_006624.1.
DR PDB; 2ZF5; X-ray; 2.40 A; O/Y=1-497.
DR PDB; 6K76; X-ray; 3.05 A; A/B=1-497.
DR PDB; 6K78; X-ray; 2.30 A; A/B/C/D=1-497.
DR PDB; 6K79; X-ray; 2.19 A; A/B/C/D=1-497.
DR PDBsum; 2ZF5; -.
DR PDBsum; 6K76; -.
DR PDBsum; 6K78; -.
DR PDBsum; 6K79; -.
DR AlphaFoldDB; O93623; -.
DR SMR; O93623; -.
DR IntAct; O93623; 1.
DR MINT; O93623; -.
DR STRING; 69014.TK1396; -.
DR EnsemblBacteria; BAD85585; BAD85585; TK1396.
DR GeneID; 3234882; -.
DR KEGG; tko:TK1396; -.
DR PATRIC; fig|69014.16.peg.1358; -.
DR eggNOG; arCOG00024; Archaea.
DR HOGENOM; CLU_009281_2_3_2; -.
DR InParanoid; O93623; -.
DR OMA; FMLMNIG; -.
DR OrthoDB; 25345at2157; -.
DR PhylomeDB; O93623; -.
DR BRENDA; 2.7.1.30; 5246.
DR UniPathway; UPA00618; UER00672.
DR EvolutionaryTrace; O93623; -.
DR Proteomes; UP000000536; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004370; F:glycerol kinase activity; ISS:UniProtKB.
DR GO; GO:0016773; F:phosphotransferase activity, alcohol group as acceptor; IBA:GO_Central.
DR GO; GO:0019563; P:glycerol catabolic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006071; P:glycerol metabolic process; ISS:UniProtKB.
DR GO; GO:0006072; P:glycerol-3-phosphate metabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0016310; P:phosphorylation; IBA:GO_Central.
DR HAMAP; MF_00186; Glycerol_kin; 1.
DR InterPro; IPR043129; ATPase_NBD.
DR InterPro; IPR000577; Carb_kinase_FGGY.
DR InterPro; IPR018485; Carb_kinase_FGGY_C.
DR InterPro; IPR018483; Carb_kinase_FGGY_CS.
DR InterPro; IPR018484; Carb_kinase_FGGY_N.
DR InterPro; IPR005999; Glycerol_kin.
DR Pfam; PF02782; FGGY_C; 1.
DR Pfam; PF00370; FGGY_N; 1.
DR PIRSF; PIRSF000538; GlpK; 1.
DR SUPFAM; SSF53067; SSF53067; 2.
DR TIGRFAMs; TIGR01311; glycerol_kin; 1.
DR PROSITE; PS00933; FGGY_KINASES_1; 1.
DR PROSITE; PS00445; FGGY_KINASES_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Direct protein sequencing; Glycerol metabolism;
KW Kinase; Nucleotide-binding; Reference proteome; Transferase.
FT CHAIN 1..497
FT /note="Glycerol kinase"
FT /id="PRO_0000059530"
FT BINDING 12..14
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00186"
FT BINDING 12
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00186"
FT BINDING 16
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00186"
FT BINDING 82..83
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00186"
FT BINDING 132
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00186"
FT BINDING 239..240
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00186"
FT BINDING 261
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00186"
FT BINDING 303
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00186"
FT BINDING 307
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00186"
FT BINDING 322
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00186"
FT BINDING 402..406
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00186"
FT CONFLICT 25
FT /note="N -> D (in Ref. 1; BAA34909)"
FT /evidence="ECO:0000305"
FT STRAND 4..10
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 12..20
FT /evidence="ECO:0007829|PDB:6K79"
FT TURN 22..24
FT /evidence="ECO:0007829|PDB:6K76"
FT STRAND 26..33
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 48..66
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 70..72
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 73..80
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 85..88
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 94..96
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 107..124
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 134..144
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 148..153
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 158..161
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 162..171
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 175..177
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 178..182
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 185..188
FT /evidence="ECO:0007829|PDB:6K79"
FT TURN 189..192
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 196..201
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 206..208
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 211..213
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 215..221
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 224..227
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 232..238
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 239..246
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 254..270
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 279..286
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 291..300
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 303..311
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 321..326
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 329..331
FT /evidence="ECO:0007829|PDB:6K78"
FT STRAND 336..338
FT /evidence="ECO:0007829|PDB:6K79"
FT TURN 346..348
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 356..358
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 366..389
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 396..401
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 402..405
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 407..417
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 421..425
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 429..441
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 444..446
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 448..454
FT /evidence="ECO:0007829|PDB:6K79"
FT STRAND 457..461
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 467..484
FT /evidence="ECO:0007829|PDB:6K79"
FT HELIX 487..490
FT /evidence="ECO:0007829|PDB:6K79"
SQ SEQUENCE 497 AA; 55904 MW; 7B55049D629CABA3 CRC64;
MEKFVLSLDE GTTSARAIIF DRESNIHGIG QYEFPQHYPR PGWVEHNPEE IWDAQLRAIK
DAIQSARIEP NQIAAIGVTN QRETTLVWDK DGKPLYNAIV WQCRRTAEMV EEIKREYGTM
IKEKTGLVPD AYFSASKLKW LLDNVPGLRE KAEKGEVMFG TVDTFLIYRL TGEHVTDYSN
ASRTMLFNIK KLDWDDELLE LFDIPESVLP EVRESSEVYG YTKKELLGAE IPVSGDAGDQ
QAALFGQAAF EAGMVKATYG TGSFILVNTD KMVLYSDNLL TTIAWGLNGR VSYALEGSIF
VTGAAVQWLR DGIKIIKHAS ETEELATKLE SNEGVYFVPA FVGLGAPYWD QFARGIIIGI
TRGTGREHLA RATLEAIAYL TRDVVDEMEK LVQIKELRVD GGATANDFLM QFQADILNRK
VIRPVVKETT ALGAAYLAGL AVDYWADTRE IAELWKAERI FEPKMDEKTR ERLYKGWKEA
VKRAMGWAKV VDSAKSN
