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DHAK_ECOLI
ID   DHAK_ECOLI              Reviewed;         356 AA.
AC   P76015;
DT   30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT   13-NOV-2007, sequence version 2.
DT   03-AUG-2022, entry version 172.
DE   RecName: Full=PEP-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK {ECO:0000303|PubMed:12813127};
DE            EC=2.7.1.121 {ECO:0000269|PubMed:11350937};
GN   Name=dhaK {ECO:0000303|PubMed:12813127}; Synonyms=ycgT;
GN   OrderedLocusNames=b1200, JW5187;
OS   Escherichia coli (strain K12).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA   Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA   Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA   Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA   Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA   Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA   Horiuchi T.;
RT   "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT   the 12.7-28.0 min region on the linkage map.";
RL   DNA Res. 3:137-155(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA   Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT   and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [4]
RP   FUNCTION, CATALYTIC ACTIVITY OF THE COMPLEX, AND BIOPHYSICOCHEMICAL
RP   PROPERTIES.
RC   STRAIN=K12;
RX   PubMed=11350937; DOI=10.1093/emboj/20.10.2480;
RA   Gutknecht R., Beutler R., Garcia-Alles L.F., Baumann U., Erni B.;
RT   "The dihydroxyacetone kinase of Escherichia coli utilizes a phosphoprotein
RT   instead of ATP as phosphoryl donor.";
RL   EMBO J. 20:2480-2486(2001).
RN   [5]
RP   INDUCTION.
RX   PubMed=15616579; DOI=10.1038/sj.emboj.7600517;
RA   Baechler C., Schneider P., Baehler P., Lustig A., Erni B.;
RT   "Escherichia coli dihydroxyacetone kinase controls gene expression by
RT   binding to transcription factor DhaR.";
RL   EMBO J. 24:283-293(2005).
RN   [6]
RP   X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) IN COMPLEX WITH DIHYDROXYACETONE
RP   ANALOG, ACTIVE SITE, SUBUNIT, AND MUTAGENESIS OF HIS-218.
RX   PubMed=12813127; DOI=10.1073/pnas.0932787100;
RA   Siebold C., Garcia-Alles L.F., Erni B., Baumann U.;
RT   "A mechanism of covalent substrate binding in the X-ray structure of
RT   subunit K of the Escherichia coli dihydroxyacetone kinase.";
RL   Proc. Natl. Acad. Sci. U.S.A. 100:8188-8192(2003).
RN   [7]
RP   X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH DIHYDROXYACETONE
RP   ANALOG, FUNCTION, ACTIVITY REGULATION, ACTIVE SITE, SUBUNIT, AND
RP   BIOPHYSICOCHEMICAL PROPERTIES.
RX   PubMed=15476397; DOI=10.1021/bi048575m;
RA   Garcia-Alles L.F., Siebold C., Luethi Nyffeler T., Fluekiger-Bruehwiler K.,
RA   Schneider P., Buergi H.-B., Baumann U., Erni B.;
RT   "Phosphoenolpyruvate- and ATP-dependent dihydroxyacetone kinases: covalent
RT   substrate-binding and kinetic mechanism.";
RL   Biochemistry 43:13037-13045(2004).
RN   [8]
RP   X-RAY CRYSTALLOGRAPHY (1.97 ANGSTROMS) OF 2-356 IN COMPLEX WITH
RP   DIHYDROXYACETONE ANALOG, MUTAGENESIS OF HIS-56; ASP-109 AND HIS-218, ACTIVE
RP   SITE, AND REACTION MECHANISM.
RX   PubMed=21209328; DOI=10.1073/pnas.1012596108;
RA   Shi R., McDonald L., Cui Q., Matte A., Cygler M., Ekiel I.;
RT   "Structural and mechanistic insight into covalent substrate binding by
RT   Escherichia coli dihydroxyacetone kinase.";
RL   Proc. Natl. Acad. Sci. U.S.A. 108:1302-1307(2011).
RN   [9]
RP   X-RAY CRYSTALLOGRAPHY (2.83 ANGSTROMS) IN COMPLEX WITH DHAR, FUNCTION,
RP   INDUCTION, AND SUBUNIT.
RX   PubMed=24440518; DOI=10.1016/j.str.2013.11.012;
RA   Shi R., McDonald L., Cygler M., Ekiel I.;
RT   "Coiled-coil helix rotation selects repressing or activating state of
RT   transcriptional regulator DhaR.";
RL   Structure 22:478-487(2014).
CC   -!- FUNCTION: Dihydroxyacetone binding subunit of the dihydroxyacetone
CC       kinase, which is responsible for the phosphoenolpyruvate (PEP)-
CC       dependent phosphorylation of dihydroxyacetone via a phosphoryl group
CC       transfer from DhaL-ATP (PubMed:15476397, PubMed:11350937). Binds
CC       covalently dihydroxyacetone in hemiaminal linkage (PubMed:15476397).
CC       DhaK acts also as corepressor of the transcription activator DhaR by
CC       binding to the sensor domain of DhaR (PubMed:24440518). In the presence
CC       of dihydroxyacetone, DhaL-ADP displaces DhaK and stimulates DhaR
CC       activity (PubMed:24440518). In the absence of dihydroxyacetone, DhaL-
CC       ADP is converted by the PTS to DhaL-ATP, which does not bind to DhaR
CC       (PubMed:24440518). {ECO:0000269|PubMed:11350937,
CC       ECO:0000269|PubMed:15476397, ECO:0000269|PubMed:24440518}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=dihydroxyacetone + phosphoenolpyruvate = dihydroxyacetone
CC         phosphate + pyruvate; Xref=Rhea:RHEA:18381, ChEBI:CHEBI:15361,
CC         ChEBI:CHEBI:16016, ChEBI:CHEBI:57642, ChEBI:CHEBI:58702;
CC         EC=2.7.1.121; Evidence={ECO:0000269|PubMed:11350937};
CC   -!- ACTIVITY REGULATION: Inhibited by chloro-3-hydroxyacetone and D,L-
CC       glyceraldehyde. {ECO:0000269|PubMed:15476397}.
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=45 uM for dihydroxyacetone {ECO:0000269|PubMed:11350937};
CC         KM=6 uM for dihydroxyacetone {ECO:0000269|PubMed:15476397};
CC         KM=110 uM for D,L-glyceraldehyde {ECO:0000269|PubMed:15476397};
CC         Note=kcat is 2.8 sec(-1) with dihydroxyacetone as substrate. Values
CC         measured with the DhaKLM complex (PubMed:11350937). kcat is 290 min(-
CC         1) with dihydroxyacetone as substrate. kcat is 12.5 min(-1) with D,L-
CC         glyceraldehyde as substrate (PubMed:15476397).
CC         {ECO:0000269|PubMed:11350937, ECO:0000269|PubMed:15476397};
CC   -!- PATHWAY: Polyol metabolism; glycerol degradation. {ECO:0000305}.
CC   -!- SUBUNIT: Homodimer (PubMed:12813127, PubMed:15476397, PubMed:24440518).
CC       The dihydroxyacetone kinase complex is composed of a homodimer of DhaM,
CC       a homodimer of DhaK and the subunit DhaL (PubMed:12813127,
CC       PubMed:15476397). DhaL also forms a complex with DhaR
CC       (PubMed:24440518). {ECO:0000269|PubMed:12813127,
CC       ECO:0000269|PubMed:15476397, ECO:0000269|PubMed:24440518}.
CC   -!- INTERACTION:
CC       P76015; P76015: dhaK; NbExp=2; IntAct=EBI-544485, EBI-544485;
CC       P76015; P76014: dhaL; NbExp=2; IntAct=EBI-544485, EBI-9021529;
CC       P76015; P76016: dhaR; NbExp=4; IntAct=EBI-544485, EBI-9153808;
CC       P76015; P60560: guaC; NbExp=2; IntAct=EBI-544485, EBI-544491;
CC       P76015; P20083: parE; NbExp=3; IntAct=EBI-544485, EBI-547277;
CC       P76015; P37624: rbbA; NbExp=2; IntAct=EBI-544485, EBI-544500;
CC   -!- INDUCTION: Activated by DhaR. {ECO:0000269|PubMed:15616579,
CC       ECO:0000269|PubMed:24440518}.
CC   -!- MISCELLANEOUS: Unlike the carbohydrate-specific transporters of the
CC       PTS, the complex DhaKML has no transport activity.
CC       {ECO:0000305|PubMed:15476397}.
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DR   EMBL; U00096; AAC74284.2; -; Genomic_DNA.
DR   EMBL; AP009048; BAA36057.2; -; Genomic_DNA.
DR   PIR; E64866; E64866.
DR   RefSeq; NP_415718.6; NC_000913.3.
DR   RefSeq; WP_000733715.1; NZ_SSZK01000010.1.
DR   PDB; 1OI2; X-ray; 1.75 A; A/B=1-356.
DR   PDB; 1OI3; X-ray; 2.00 A; A/B=1-356.
DR   PDB; 1UOD; X-ray; 1.90 A; A/B=1-356.
DR   PDB; 1UOE; X-ray; 2.00 A; A/B=1-356.
DR   PDB; 3PNK; X-ray; 2.21 A; A/B=2-356.
DR   PDB; 3PNL; X-ray; 2.20 A; A=2-356.
DR   PDB; 3PNM; X-ray; 2.55 A; A/B/C/D=2-356.
DR   PDB; 3PNO; X-ray; 1.97 A; A/B/C/D=2-356.
DR   PDB; 3PNQ; X-ray; 2.20 A; A/B/C/D=2-356.
DR   PDB; 4LRX; X-ray; 3.25 A; A/B=1-356.
DR   PDB; 4LRY; X-ray; 2.83 A; A/B=1-356.
DR   PDBsum; 1OI2; -.
DR   PDBsum; 1OI3; -.
DR   PDBsum; 1UOD; -.
DR   PDBsum; 1UOE; -.
DR   PDBsum; 3PNK; -.
DR   PDBsum; 3PNL; -.
DR   PDBsum; 3PNM; -.
DR   PDBsum; 3PNO; -.
DR   PDBsum; 3PNQ; -.
DR   PDBsum; 4LRX; -.
DR   PDBsum; 4LRY; -.
DR   AlphaFoldDB; P76015; -.
DR   SMR; P76015; -.
DR   BioGRID; 4260718; 14.
DR   BioGRID; 850114; 3.
DR   ComplexPortal; CPX-2634; Dha Kinase.
DR   DIP; DIP-11563N; -.
DR   IntAct; P76015; 7.
DR   STRING; 511145.b1200; -.
DR   MoonProt; P76015; -.
DR   jPOST; P76015; -.
DR   PaxDb; P76015; -.
DR   PRIDE; P76015; -.
DR   EnsemblBacteria; AAC74284; AAC74284; b1200.
DR   EnsemblBacteria; BAA36057; BAA36057; BAA36057.
DR   GeneID; 945747; -.
DR   KEGG; ecj:JW5187; -.
DR   KEGG; eco:b1200; -.
DR   PATRIC; fig|1411691.4.peg.1085; -.
DR   EchoBASE; EB3660; -.
DR   eggNOG; COG2376; Bacteria.
DR   HOGENOM; CLU_017054_0_0_6; -.
DR   InParanoid; P76015; -.
DR   OMA; MLSAACP; -.
DR   PhylomeDB; P76015; -.
DR   BioCyc; EcoCyc:G6627-MON; -.
DR   BioCyc; MetaCyc:G6627-MON; -.
DR   BRENDA; 2.7.1.121; 2026.
DR   BRENDA; 2.7.1.29; 2026.
DR   SABIO-RK; P76015; -.
DR   UniPathway; UPA00616; -.
DR   EvolutionaryTrace; P76015; -.
DR   PRO; PR:P76015; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR   GO; GO:1990234; C:transferase complex; IPI:ComplexPortal.
DR   GO; GO:0004371; F:glycerone kinase activity; IBA:GO_Central.
DR   GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR   GO; GO:0047324; F:phosphoenolpyruvate-glycerone phosphotransferase activity; IMP:EcoCyc.
DR   GO; GO:0046835; P:carbohydrate phosphorylation; IDA:ComplexPortal.
DR   GO; GO:0006974; P:cellular response to DNA damage stimulus; IEP:EcoliWiki.
DR   GO; GO:0019563; P:glycerol catabolic process; IBA:GO_Central.
DR   GO; GO:0061610; P:glycerol to glycerone phosphate metabolic process; IMP:EcoCyc.
DR   GO; GO:0042182; P:ketone catabolic process; IMP:EcoCyc.
DR   GO; GO:0046365; P:monosaccharide catabolic process; IMP:EcoCyc.
DR   GO; GO:0006090; P:pyruvate metabolic process; IDA:ComplexPortal.
DR   InterPro; IPR012736; DhaK_1.
DR   InterPro; IPR004006; DhaK_dom.
DR   Pfam; PF02733; Dak1; 1.
DR   TIGRFAMs; TIGR02363; dhaK1; 1.
DR   PROSITE; PS51481; DHAK; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Glycerol metabolism; Kinase; Reference proteome; Transferase.
FT   CHAIN           1..356
FT                   /note="PEP-dependent dihydroxyacetone kinase,
FT                   dihydroxyacetone-binding subunit DhaK"
FT                   /id="PRO_0000121529"
FT   DOMAIN          7..352
FT                   /note="DhaK"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00814"
FT   ACT_SITE        56
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000305|PubMed:21209328"
FT   ACT_SITE        218
FT                   /note="Tele-hemiaminal-histidine intermediate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00814,
FT                   ECO:0000269|PubMed:12813127, ECO:0000269|PubMed:15476397,
FT                   ECO:0000269|PubMed:21209328, ECO:0007744|PDB:1OI2,
FT                   ECO:0007744|PDB:1UOD, ECO:0007744|PDB:1UOE,
FT                   ECO:0007744|PDB:3PNK, ECO:0007744|PDB:3PNL,
FT                   ECO:0007744|PDB:3PNQ"
FT   BINDING         53..56
FT                   /ligand="dihydroxyacetone"
FT                   /ligand_id="ChEBI:CHEBI:16016"
FT                   /evidence="ECO:0000269|PubMed:12813127,
FT                   ECO:0000269|PubMed:15476397, ECO:0000269|PubMed:21209328,
FT                   ECO:0007744|PDB:1OI2, ECO:0007744|PDB:1UOD,
FT                   ECO:0007744|PDB:1UOE, ECO:0007744|PDB:3PNK,
FT                   ECO:0007744|PDB:3PNL, ECO:0007744|PDB:3PNQ"
FT   BINDING         104
FT                   /ligand="dihydroxyacetone"
FT                   /ligand_id="ChEBI:CHEBI:16016"
FT                   /evidence="ECO:0000269|PubMed:12813127,
FT                   ECO:0000269|PubMed:21209328, ECO:0007744|PDB:1OI2,
FT                   ECO:0007744|PDB:3PNK, ECO:0007744|PDB:3PNL,
FT                   ECO:0007744|PDB:3PNQ"
FT   BINDING         109
FT                   /ligand="dihydroxyacetone"
FT                   /ligand_id="ChEBI:CHEBI:16016"
FT                   /evidence="ECO:0000269|PubMed:12813127,
FT                   ECO:0000269|PubMed:15476397, ECO:0000269|PubMed:21209328,
FT                   ECO:0007744|PDB:1OI2, ECO:0007744|PDB:1UOD,
FT                   ECO:0007744|PDB:1UOE, ECO:0007744|PDB:3PNK,
FT                   ECO:0007744|PDB:3PNL, ECO:0007744|PDB:3PNQ"
FT   MUTAGEN         56
FT                   /note="H->A,N: Shows a moderate decrease in the catalytic
FT                   efficiency but at least a 40- to 300-fold increase in
FT                   affinity for dihydroxyacetone."
FT                   /evidence="ECO:0000269|PubMed:21209328"
FT   MUTAGEN         109
FT                   /note="D->A,N: Loss of kinase activity."
FT                   /evidence="ECO:0000269|PubMed:21209328"
FT   MUTAGEN         218
FT                   /note="H->A,K: Loss of kinase activity."
FT                   /evidence="ECO:0000269|PubMed:12813127,
FT                   ECO:0000269|PubMed:21209328"
FT   HELIX           8..10
FT                   /evidence="ECO:0007829|PDB:3PNL"
FT   HELIX           11..22
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          26..29
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   TURN            30..33
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          34..37
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          47..56
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   TURN            57..60
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   HELIX           61..63
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          64..66
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          68..77
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   HELIX           83..93
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          99..106
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   HELIX           107..122
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          127..132
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          140..142
FT                   /evidence="ECO:0007829|PDB:3PNK"
FT   STRAND          145..147
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   HELIX           152..166
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   HELIX           170..181
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          184..192
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   TURN            197..199
FT                   /evidence="ECO:0007829|PDB:3PNL"
FT   STRAND          201..203
FT                   /evidence="ECO:0007829|PDB:4LRY"
FT   STRAND          210..213
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          217..219
FT                   /evidence="ECO:0007829|PDB:3PNK"
FT   STRAND          223..227
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   HELIX           231..244
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          248..256
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   TURN            257..260
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          261..269
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          277..284
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          286..288
FT                   /evidence="ECO:0007829|PDB:3PNL"
FT   HELIX           290..307
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          310..317
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          325..335
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   HELIX           337..344
FT                   /evidence="ECO:0007829|PDB:1OI2"
FT   STRAND          347..351
FT                   /evidence="ECO:0007829|PDB:1OI2"
SQ   SEQUENCE   356 AA;  38215 MW;  510D73BE9685395F CRC64;
     MKKLINDVQD VLDEQLAGLA KAHPSLTLHQ DPVYVTRADA PVAGKVALLS GGGSGHEPMH
     CGYIGQGMLS GACPGEIFTS PTPDKIFECA MQVDGGEGVL LIIKNYTGDI LNFETATELL
     HDSGVKVTTV VIDDDVAVKD SLYTAGRRGV ANTVLIEKLV GAAAERGDSL DACAELGRKL
     NNQGHSIGIA LGACTVPAAG KPSFTLADNE MEFGVGIHGE PGIDRRPFSS LDQTVDEMFD
     TLLVNGSYHR TLRFWDYQQG SWQEEQQTKQ PLQSGDRVIA LVNNLGATPL SELYGVYNRL
     TTRCQQAGLT IERNLIGAYC TSLDMTGFSI TLLKVDDETL ALWDAPVHTP ALNWGK
 
 
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