KDGK_SULTO
ID KDGK_SULTO Reviewed; 311 AA.
AC Q96XN9;
DT 22-APR-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=2-dehydro-3-deoxygluconokinase {ECO:0000305};
DE EC=2.7.1.45 {ECO:0000269|PubMed:17407821};
DE AltName: Full=2-keto-3-deoxy-D-gluconate kinase {ECO:0000303|PubMed:17407821};
DE Short=KDG kinase {ECO:0000305};
DE Short=KDGK {ECO:0000303|PubMed:17407821};
GN Name=kdgK {ECO:0000312|EMBL:BAB67588.1};
GN Synonyms=ST2478 {ECO:0000312|EMBL:BAB67588.1};
GN OrderedLocusNames=STK_24780 {ECO:0000312|EMBL:BAB67588.1};
OS Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
OS (Sulfolobus tokodaii).
OC Archaea; Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae;
OC Sulfurisphaera.
OX NCBI_TaxID=273063;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 16993 / JCM 10545 / NBRC 100140 / 7;
RX PubMed=11572479; DOI=10.1093/dnares/8.4.123;
RA Kawarabayasi Y., Hino Y., Horikawa H., Jin-no K., Takahashi M., Sekine M.,
RA Baba S., Ankai A., Kosugi H., Hosoyama A., Fukui S., Nagai Y.,
RA Nishijima K., Otsuka R., Nakazawa H., Takamiya M., Kato Y., Yoshizawa T.,
RA Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K.,
RA Masuda S., Yanagii M., Nishimura M., Yamagishi A., Oshima T., Kikuchi H.;
RT "Complete genome sequence of an aerobic thermoacidophilic Crenarchaeon,
RT Sulfolobus tokodaii strain7.";
RL DNA Res. 8:123-140(2001).
RN [2]
RP PROTEIN SEQUENCE OF 1-6, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=17407821; DOI=10.1016/j.pep.2007.02.013;
RA Ohshima T., Kawakami R., Kanai Y., Goda S., Sakuraba H.;
RT "Gene expression and characterization of 2-keto-3-deoxygluconate kinase, a
RT key enzyme in the modified Entner-Doudoroff pathway of the aerobic and
RT acidophilic hyperthermophile Sulfolobus tokodaii.";
RL Protein Expr. Purif. 54:73-78(2007).
RN [3] {ECO:0007744|PDB:1WYE}
RP X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS).
RA Toyoda T., Suzuki K., Hossain M.T., Koike I., Sekiguchi T., Takenaka A.;
RT "Crystal structure of 2-keto-3-deoxygluconate kinase from Sulfolobus
RT tokodaii.";
RL Submitted (FEB-2005) to the PDB data bank.
RN [4] {ECO:0007744|PDB:2DCN}
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) IN COMPLEX WITH
RP 2-KETO-6-PHOSPHATE-D-GLUCONIC ACID AND ADP.
RA Okazaki S., Onda H., Suzuki A., Kuramitsu S., Masui R., Yamane T.;
RT "Crystal structure of 2-keto-3-deoxygluconate kinase from Sulfolobus
RT tokodaii complexed with 2-keto-6-phosphogluconate.";
RL Submitted (JAN-2006) to the PDB data bank.
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). Can also use GTP, but not ADP or AMP, as a
CC phosphoryl donor and 2-keto-D-gluconate (KG) as a phosphoryl acceptor.
CC {ECO:0000269|PubMed:17407821}.
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:17407821};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14798;
CC Evidence={ECO:0000269|PubMed:17407821};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000269|PubMed:17407821};
CC Note=Mg(2+) is the most effective ion, but it can be replaced with
CC Co(2+), Ni(2+), Zn(2+) or Mn(2+). {ECO:0000269|PubMed:17407821};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.027 mM for KDG (at 50 degrees Celsius)
CC {ECO:0000269|PubMed:17407821};
CC KM=1.3 mM for KG (at 50 degrees Celsius)
CC {ECO:0000269|PubMed:17407821};
CC KM=0.036 mM for ATP (at 50 degrees Celsius, in the presence of KDG)
CC {ECO:0000269|PubMed:17407821};
CC KM=0.11 mM for ATP (at 50 degrees Celsius, in the presence of KG)
CC {ECO:0000269|PubMed:17407821};
CC Vmax=4.13 umol/min/mg enzyme with KDG as substrate
CC {ECO:0000269|PubMed:17407821};
CC Vmax=13.26 umol/min/mg enzyme with KG as substrate
CC {ECO:0000269|PubMed:17407821};
CC Note=kcat is 8.26 sec(-1) with KDG as substrate. kcat is 26.3 sec(-1)
CC with KG as substrate. {ECO:0000269|PubMed:17407821};
CC pH dependence:
CC Optimum pH is around 8.5. {ECO:0000269|PubMed:17407821};
CC Temperature dependence:
CC Optimum temperature is 80 degrees Celsius. Extremely thermostable.
CC {ECO:0000269|PubMed:17407821};
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. {ECO:0000305}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:17407821}.
CC -!- SIMILARITY: Belongs to the carbohydrate kinase PfkB family.
CC {ECO:0000305}.
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DR EMBL; BA000023; BAB67588.1; -; Genomic_DNA.
DR RefSeq; WP_010980563.1; NC_003106.2.
DR PDB; 1WYE; X-ray; 2.80 A; A/B/C/D/E/F=1-311.
DR PDB; 2DCN; X-ray; 2.25 A; A/B/C/D/E/F/G/H/I/J/K/L=1-311.
DR PDBsum; 1WYE; -.
DR PDBsum; 2DCN; -.
DR AlphaFoldDB; Q96XN9; -.
DR SMR; Q96XN9; -.
DR STRING; 273063.STK_24780; -.
DR EnsemblBacteria; BAB67588; BAB67588; STK_24780.
DR GeneID; 1460561; -.
DR KEGG; sto:STK_24780; -.
DR PATRIC; fig|273063.9.peg.2799; -.
DR eggNOG; arCOG00014; Archaea.
DR OMA; MAMFYAN; -.
DR OrthoDB; 36944at2157; -.
DR BRENDA; 2.7.1.45; 15396.
DR UniPathway; UPA00856; UER00828.
DR EvolutionaryTrace; Q96XN9; -.
DR Proteomes; UP000001015; Chromosome.
DR GO; GO:0008673; F:2-dehydro-3-deoxygluconokinase activity; IEA:UniProtKB-EC.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR Gene3D; 3.40.1190.20; -; 1.
DR InterPro; IPR011611; PfkB_dom.
DR InterPro; IPR029056; Ribokinase-like.
DR Pfam; PF00294; PfkB; 1.
DR SUPFAM; SSF53613; SSF53613; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Carbohydrate metabolism;
KW Direct protein sequencing; Kinase; Nucleotide-binding; Reference proteome;
KW Transferase.
FT CHAIN 1..311
FT /note="2-dehydro-3-deoxygluconokinase"
FT /id="PRO_0000449271"
FT ACT_SITE 256
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q97U29"
FT BINDING 34..35
FT /ligand="substrate"
FT /evidence="ECO:0000305|Ref.4"
FT BINDING 106..108
FT /ligand="substrate"
FT /evidence="ECO:0000305|Ref.4"
FT BINDING 164..166
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q97U29"
FT BINDING 166
FT /ligand="substrate"
FT /evidence="ECO:0000305|Ref.4"
FT BINDING 224..229
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|Ref.4"
FT BINDING 253..256
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q97U29"
FT BINDING 253
FT /ligand="substrate"
FT /evidence="ECO:0000305|Ref.4"
FT BINDING 256
FT /ligand="substrate"
FT /evidence="ECO:0000305|Ref.4"
FT BINDING 283
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|Ref.4"
FT BINDING 292
FT /ligand="substrate"
FT /evidence="ECO:0000305|Ref.4"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:2DCN"
FT STRAND 11..20
FT /evidence="ECO:0007829|PDB:2DCN"
FT HELIX 22..24
FT /evidence="ECO:0007829|PDB:2DCN"
FT STRAND 27..33
FT /evidence="ECO:0007829|PDB:2DCN"
FT HELIX 35..45
FT /evidence="ECO:0007829|PDB:2DCN"
FT STRAND 49..53
FT /evidence="ECO:0007829|PDB:2DCN"
FT STRAND 55..59
FT /evidence="ECO:0007829|PDB:2DCN"
FT HELIX 60..71
FT /evidence="ECO:0007829|PDB:2DCN"
FT STRAND 80..82
FT /evidence="ECO:0007829|PDB:2DCN"
FT STRAND 89..95
FT /evidence="ECO:0007829|PDB:2DCN"
FT STRAND 102..107
FT /evidence="ECO:0007829|PDB:2DCN"
FT HELIX 113..115
FT /evidence="ECO:0007829|PDB:2DCN"
FT HELIX 118..120
FT /evidence="ECO:0007829|PDB:2DCN"
FT HELIX 123..126
FT /evidence="ECO:0007829|PDB:2DCN"
FT STRAND 130..135
FT /evidence="ECO:0007829|PDB:2DCN"
FT HELIX 136..140
FT /evidence="ECO:0007829|PDB:2DCN"
FT HELIX 143..155
FT /evidence="ECO:0007829|PDB:2DCN"
FT STRAND 157..162
FT /evidence="ECO:0007829|PDB:2DCN"
FT TURN 167..169
FT /evidence="ECO:0007829|PDB:2DCN"
FT HELIX 172..185
FT /evidence="ECO:0007829|PDB:2DCN"
FT STRAND 188..194
FT /evidence="ECO:0007829|PDB:2DCN"
FT HELIX 195..202
FT /evidence="ECO:0007829|PDB:2DCN"
FT HELIX 207..214
FT /evidence="ECO:0007829|PDB:2DCN"
FT TURN 215..217
FT /evidence="ECO:0007829|PDB:2DCN"
FT STRAND 218..226
FT /evidence="ECO:0007829|PDB:2DCN"
FT STRAND 229..234
FT /evidence="ECO:0007829|PDB:2DCN"
FT STRAND 237..242
FT /evidence="ECO:0007829|PDB:2DCN"
FT HELIX 254..266
FT /evidence="ECO:0007829|PDB:2DCN"
FT TURN 267..269
FT /evidence="ECO:0007829|PDB:2DCN"
FT HELIX 272..286
FT /evidence="ECO:0007829|PDB:2DCN"
FT STRAND 289..293
FT /evidence="ECO:0007829|PDB:2DCN"
FT HELIX 299..308
FT /evidence="ECO:0007829|PDB:2DCN"
SQ SEQUENCE 311 AA; 34480 MW; 670DA66756FA3903 CRC64;
MAKLITLGEI LIEFNALSPG PLRHVSYFEK HVAGSEANYC VAFIKQGNEC GIIAKVGDDE
FGYNAIEWLR GQGVDVSHMK IDPSAPTGIF FIQRHYPVPL KSESIYYRKG SAGSKLSPED
VDEEYVKSAD LVHSSGITLA ISSTAKEAVY KAFEIASNRS FDTNIRLKLW SAEEAKREIL
KLLSKFHLKF LITDTDDSKI ILGESDPDKA AKAFSDYAEI IVMKLGPKGA IVYYDGKKYY
SSGYQVPVED VTGAGDALGG TFLSLYYKGF EMEKALDYAI VASTLNVMIR GDQENLPTTK
DIETFLREMK K
