KDGK_THET8
ID KDGK_THET8 Reviewed; 309 AA.
AC Q53W83;
DT 26-JUN-2013, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 98.
DE RecName: Full=2-dehydro-3-deoxygluconokinase;
DE EC=2.7.1.45;
DE AltName: Full=2-keto-3-deoxygluconokinase;
DE AltName: Full=3-deoxy-2-oxo-D-gluconate kinase;
DE AltName: Full=KDG kinase;
GN Name=kdgK; OrderedLocusNames=TTHB079;
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OG Plasmid pTT27.
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH
RP 2-KETO-3-DEOXYGLUCONATE AND ATP, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE,
RP BIOPHYSICOCHEMICAL PROPERTIES, REACTION MECHANISM, AND SUBUNIT.
RX PubMed=15210349; DOI=10.1016/j.jmb.2004.04.074;
RA Ohshima N., Inagaki E., Yasuike K., Takio K., Tahirov T.H.;
RT "Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence
RT for recognition of an open chain substrate.";
RL J. Mol. Biol. 340:477-489(2004).
CC -!- FUNCTION: Involved in the degradation of glucose via the semi-
CC phosphorylative Entner-Doudoroff pathway. Catalyzes the phosphorylation
CC of 2-keto-3-deoxygluconate (KDG) to produce 2-keto-3-deoxy-6-
CC phosphogluconate (KDPG). {ECO:0000269|PubMed:15210349}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-dehydro-3-deoxy-D-gluconate + ATP = 2-dehydro-3-deoxy-6-
CC phospho-D-gluconate + ADP + H(+); Xref=Rhea:RHEA:14797,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:57569,
CC ChEBI:CHEBI:57990, ChEBI:CHEBI:456216; EC=2.7.1.45;
CC Evidence={ECO:0000269|PubMed:15210349};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.32 mM for KDG (at 35 degrees Celsius and pH 7.4)
CC {ECO:0000269|PubMed:15210349};
CC KM=3.6 mM for 2-keto-D-gluconate (at 35 degrees Celsius and pH 7.4)
CC {ECO:0000269|PubMed:15210349};
CC Note=kcat is 11 sec(-1) for KDG and 2.2 sec(-1) for 2-keto-D-
CC gluconate (at 35 degrees Celsius and pH 7.4).;
CC pH dependence:
CC Optimum pH is between 6 and 9. {ECO:0000269|PubMed:15210349};
CC -!- PATHWAY: Carbohydrate acid metabolism; 2-dehydro-3-deoxy-D-gluconate
CC degradation; D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-
CC 3-deoxy-D-gluconate: step 1/2.
CC -!- SUBUNIT: Homohexamer; trimer of dimers. {ECO:0000269|PubMed:15210349}.
CC -!- SIMILARITY: Belongs to the carbohydrate kinase pfkB family.
CC {ECO:0000305}.
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DR EMBL; AP008227; BAD71875.1; -; Genomic_DNA.
DR RefSeq; WP_011229211.1; NC_006462.1.
DR RefSeq; YP_145318.1; NC_006462.1.
DR PDB; 1V19; X-ray; 2.30 A; A/B=1-309.
DR PDB; 1V1A; X-ray; 2.10 A; A/B=1-309.
DR PDB; 1V1B; X-ray; 2.60 A; A/B/C/D=1-309.
DR PDB; 1V1S; X-ray; 3.20 A; A/B/C/D/E/F=1-309.
DR PDBsum; 1V19; -.
DR PDBsum; 1V1A; -.
DR PDBsum; 1V1B; -.
DR PDBsum; 1V1S; -.
DR AlphaFoldDB; Q53W83; -.
DR SMR; Q53W83; -.
DR PRIDE; Q53W83; -.
DR EnsemblBacteria; BAD71875; BAD71875; BAD71875.
DR GeneID; 3167896; -.
DR KEGG; ttj:TTHB079; -.
DR PATRIC; fig|300852.9.peg.2023; -.
DR HOGENOM; CLU_027634_6_0_0; -.
DR OMA; MAMFYAN; -.
DR PhylomeDB; Q53W83; -.
DR UniPathway; UPA00856; UER00828.
DR EvolutionaryTrace; Q53W83; -.
DR Proteomes; UP000000532; Plasmid pTT27.
DR GO; GO:0008673; F:2-dehydro-3-deoxygluconokinase activity; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IDA:UniProtKB.
DR GO; GO:0000166; F:nucleotide binding; IDA:UniProtKB.
DR GO; GO:0016310; P:phosphorylation; IDA:UniProtKB.
DR Gene3D; 3.40.1190.20; -; 1.
DR InterPro; IPR002173; Carboh/pur_kinase_PfkB_CS.
DR InterPro; IPR011611; PfkB_dom.
DR InterPro; IPR002139; Ribo/fructo_kinase.
DR InterPro; IPR029056; Ribokinase-like.
DR Pfam; PF00294; PfkB; 1.
DR PRINTS; PR00990; RIBOKINASE.
DR SUPFAM; SSF53613; SSF53613; 1.
DR PROSITE; PS00584; PFKB_KINASES_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Carbohydrate metabolism; Kinase;
KW Nucleotide-binding; Plasmid; Reference proteome; Transferase.
FT CHAIN 1..309
FT /note="2-dehydro-3-deoxygluconokinase"
FT /id="PRO_0000422662"
FT ACT_SITE 251
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:15210349"
FT BINDING 34..38
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15210349"
FT BINDING 89
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q97U29"
FT BINDING 103..105
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15210349"
FT BINDING 165..167
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q97U29"
FT BINDING 167
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15210349"
FT BINDING 193
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:15210349"
FT BINDING 219..225
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:15210349"
FT BINDING 248..251
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:15210349"
FT BINDING 251
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15210349"
FT BINDING 275
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:15210349"
FT BINDING 287
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15210349"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:1V1A"
FT STRAND 11..15
FT /evidence="ECO:0007829|PDB:1V1A"
FT STRAND 17..20
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 22..24
FT /evidence="ECO:0007829|PDB:1V1A"
FT STRAND 27..33
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 35..45
FT /evidence="ECO:0007829|PDB:1V1A"
FT STRAND 50..56
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 60..72
FT /evidence="ECO:0007829|PDB:1V1A"
FT STRAND 79..81
FT /evidence="ECO:0007829|PDB:1V1A"
FT STRAND 88..93
FT /evidence="ECO:0007829|PDB:1V1A"
FT STRAND 99..104
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 110..112
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 120..123
FT /evidence="ECO:0007829|PDB:1V1A"
FT STRAND 127..132
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 140..154
FT /evidence="ECO:0007829|PDB:1V1A"
FT TURN 155..157
FT /evidence="ECO:0007829|PDB:1V1A"
FT STRAND 159..163
FT /evidence="ECO:0007829|PDB:1V1A"
FT TURN 168..170
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 173..183
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 184..186
FT /evidence="ECO:0007829|PDB:1V1A"
FT STRAND 188..193
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 194..201
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 204..210
FT /evidence="ECO:0007829|PDB:1V1A"
FT STRAND 214..219
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 221..223
FT /evidence="ECO:0007829|PDB:1V1A"
FT STRAND 225..229
FT /evidence="ECO:0007829|PDB:1V1A"
FT STRAND 232..235
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 249..262
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 267..282
FT /evidence="ECO:0007829|PDB:1V1A"
FT TURN 286..290
FT /evidence="ECO:0007829|PDB:1V1A"
FT HELIX 294..297
FT /evidence="ECO:0007829|PDB:1V1A"
SQ SEQUENCE 309 AA; 33430 MW; AC817D04B2B0A19B CRC64;
MLEVVTAGEP LVALVPQEPG HLRGKRLLEV YVGGAEVNVA VALARLGVKV GFVGRVGEDE
LGAMVEERLR AEGVDLTHFR RAPGFTGLYL REYLPLGQGR VFYYRKGSAG SALAPGAFDP
DYLEGVRFLH LSGITPALSP EARAFSLWAM EEAKRRGVRV SLDVNYRQTL WSPEEARGFL
ERALPGVDLL FLSEEEAELL FGRVEEALRA LSAPEVVLKR GAKGAWAFVD GRRVEGSAFA
VEAVDPVGAG DAFAAGYLAG AVWGLPVEER LRLANLLGAS VAASRGDHEG APYREDLEVL
LKATQTFMR
