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 27-NOV-2024, entry version 183.
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; Pseudomonadota; 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:11350937, PubMed:15476397). 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; 16.
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; 511145-b1200; -.
DR EnsemblBacteria; AAC74284; AAC74284; b1200.
DR GeneID; 945747; -.
DR KEGG; ecj:JW5187; -.
DR KEGG; eco:b1200; -.
DR KEGG; ecoc:C3026_07055; -.
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 OrthoDB; 9806345at2; -.
DR PhylomeDB; P76015; -.
DR BioCyc; EcoCyc:G6627-MONOMER; -.
DR BioCyc; MetaCyc:G6627-MONOMER; -.
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:0042803; F:protein homodimerization activity; IDA:EcoCyc.
DR GO; GO:0046835; P:carbohydrate phosphorylation; IDA:ComplexPortal.
DR GO; GO:0006974; P:DNA damage response; 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 FunFam; 3.30.1180.20:FF:000002; Dihydroxyacetone kinase subunit DhaK; 1.
DR FunFam; 3.40.50.10440:FF:000001; Dihydroxyacetone kinase, DhaK subunit; 1.
DR InterPro; IPR012736; DhaK_1.
DR InterPro; IPR004006; DhaK_dom.
DR InterPro; IPR050861; Dihydroxyacetone_Kinase.
DR NCBIfam; TIGR02363; dhaK1; 1.
DR PANTHER; PTHR28629; TRIOKINASE/FMN CYCLASE; 1.
DR PANTHER; PTHR28629:SF4; TRIOKINASE_FMN CYCLASE; 1.
DR Pfam; PF02733; Dak1; 1.
DR SUPFAM; SSF82549; DAK1/DegV-like; 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
//
