ID   XYLB_ECOLI              Reviewed;         484 AA.
AC   P09099; Q2M7M7;
DT   01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT   01-JUL-1989, sequence version 1.
DT   04-NOV-2026, entry version 169.
DE   RecName: Full=Xylulose kinase {ECO:0000255|HAMAP-Rule:MF_02220, ECO:0000303|PubMed:6320721};
DE            Short=XK {ECO:0000303|PubMed:17123542};
DE            Short=Xylulokinase {ECO:0000255|HAMAP-Rule:MF_02220, ECO:0000303|PubMed:11168365};
DE            EC=2.7.1.17 {ECO:0000255|HAMAP-Rule:MF_02220, ECO:0000269|PubMed:17123542};
DE   AltName: Full=1-deoxy-D-xylulokinase {ECO:0000303|PubMed:11168365};
DE            EC=2.7.1.- {ECO:0000269|PubMed:11168365};
GN   Name=xylB {ECO:0000255|HAMAP-Rule:MF_02220};
GN   OrderedLocusNames=b3564, JW3536;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC   Enterobacterales; Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=K12 / MM294 / ATCC 33625 / DSM 5208;
RX   PubMed=6320721; DOI=10.1128/aem.47.1.15-21.1984;
RA   Lawlis V.B., Dennis M.S., Chen E.Y., Smith D.H., Henner D.J.;
RT   "Cloning and sequencing of the xylose isomerase and xylulose kinase genes
RT   of Escherichia coli.";
RL   Appl. Environ. Microbiol. 47:15-21(1984).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=8041620; DOI=10.1093/nar/22.13.2576;
RA   Sofia H.J., Burland V., Daniels D.L., Plunkett G. III, Blattner F.R.;
RT   "Analysis of the Escherichia coli genome. V. DNA sequence of the region
RT   from 76.0 to 81.5 minutes.";
RL   Nucleic Acids Res. 22:2576-2586(1994).
RN   [3]
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   [4]
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   [5]
RP   IDENTIFICATION BY 2D-GEL.
RX   PubMed=9298644; DOI=10.1002/elps.1150180805;
RA   VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT   "Escherichia coli proteome analysis using the gene-protein database.";
RL   Electrophoresis 18:1243-1251(1997).
RN   [6]
RP   PROTEIN SEQUENCE OF 1-21, FUNCTION, AND CATALYTIC ACTIVITY.
RX   PubMed=11168365; DOI=10.1046/j.1432-1033.2001.01875.x;
RA   Wungsintaweekul J., Herz S., Hecht S., Eisenreich W., Feicht R.,
RA   Rohdich F., Bacher A., Zenk M.H.;
RT   "Phosphorylation of 1-deoxy-D-xylulose by D-xylulokinase of Escherichia
RT   coli.";
RL   Eur. J. Biochem. 268:310-316(2001).
RN   [7] {ECO:0007744|PDB:2ITM, ECO:0007744|PDB:2NLX}
RP   X-RAY CRYSTALLOGRAPHY OF APOENZYME AND IN COMPLEX WITH D-XYLULOSE,
RP   FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL
RP   PROPERTIES, SUBUNIT, ACTIVE SITE, AND MUTAGENESIS OF ASP-6 AND ASP-233.
RX   PubMed=17123542; DOI=10.1016/j.jmb.2006.10.068;
RA   Di Luccio E., Petschacher B., Voegtli J., Chou H.T., Stahlberg H.,
RA   Nidetzky B., Wilson D.K.;
RT   "Structural and kinetic studies of induced fit in xylulose kinase from
RT   Escherichia coli.";
RL   J. Mol. Biol. 365:783-798(2007).
CC   -!- FUNCTION: Catalyzes the phosphorylation of D-xylulose to D-xylulose 5-
CC       phosphate (PubMed:17123542). Also catalyzes the phosphorylation of 1-
CC       deoxy-D-xylulose to 1-deoxy-D-xylulose 5-phosphate, with lower
CC       efficiency (PubMed:11168365). Can also use D-ribulose, xylitol and D-
CC       arabitol, but D-xylulose is preferred over the other substrates
CC       (PubMed:17123542). Has a weak substrate-independent Mg-ATP-hydrolyzing
CC       activity (PubMed:17123542). {ECO:0000269|PubMed:11168365,
CC       ECO:0000269|PubMed:17123542}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=D-xylulose + ATP = D-xylulose 5-phosphate + ADP + H(+);
CC         Xref=Rhea:RHEA:10964, ChEBI:CHEBI:15378, ChEBI:CHEBI:17140,
CC         ChEBI:CHEBI:30616, ChEBI:CHEBI:57737, ChEBI:CHEBI:456216;
CC         EC=2.7.1.17; Evidence={ECO:0000255|HAMAP-Rule:MF_02220,
CC         ECO:0000269|PubMed:17123542};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=1-deoxy-D-xylulose + ATP = 1-deoxy-D-xylulose 5-phosphate +
CC         ADP + H(+); Xref=Rhea:RHEA:27990, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:28354, ChEBI:CHEBI:30616, ChEBI:CHEBI:57792,
CC         ChEBI:CHEBI:456216; Evidence={ECO:0000269|PubMed:11168365};
CC   -!- ACTIVITY REGULATION: Sugar binding is accompanied by a dramatic hinge-
CC       bending movement that enhances interactions with Mg-ATP.
CC       {ECO:0000269|PubMed:17123542}.
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=0.29 mM for D-xylulose {ECO:0000269|PubMed:17123542};
CC         KM=14 mM for D-ribulose {ECO:0000269|PubMed:17123542};
CC         KM=127 mM for xylitol {ECO:0000269|PubMed:17123542};
CC         KM=141 mM for D-arabitol {ECO:0000269|PubMed:17123542};
CC         Note=kcat is 255 sec(-1) with D-xylulose as substrate. kcat is 235
CC         sec(-1) with D-ribulose as substrate. kcat is 237 sec(-1) with
CC         xylitol as substrate. kcat is 105 sec(-1) with D-arabitol as
CC         substrate. {ECO:0000269|PubMed:17123542};
CC   -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:17123542}.
CC   -!- SIMILARITY: Belongs to the FGGY kinase family. {ECO:0000255|HAMAP-
CC       Rule:MF_02220, ECO:0000305}.
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DR   EMBL; K01996; AAA24769.1; -; Genomic_DNA.
DR   EMBL; X04691; CAA28395.1; -; Genomic_DNA.
DR   EMBL; U00039; AAB18541.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC76588.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAE77729.1; -; Genomic_DNA.
DR   PIR; A30266; KIECXY.
DR   RefSeq; NP_418021.1; NC_000913.3.
DR   RefSeq; WP_000275334.1; NZ_CP010445.1.
DR   PDB; 2ITM; X-ray; 2.10 A; A/B=1-484.
DR   PDB; 2NLX; X-ray; 2.70 A; A/B=1-484.
DR   AlphaFoldDB; P09099; -.
DR   SMR; P09099; -.
DR   BioGRID; 4262539; 12.
DR   FunCoup; P09099; 173.
DR   IntAct; P09099; 1.
DR   STRING; 511145.b3564; -.
DR   jPOST; P09099; -.
DR   PaxDb; 511145-b3564; -.
DR   EnsemblBacteria; AAC76588; AAC76588; b3564.
DR   GeneID; 948133; -.
DR   KEGG; ecj:JW3536; -.
DR   KEGG; eco:b3564; -.
DR   KEGG; ecoc:C3026_19325; -.
DR   PATRIC; fig|1411691.4.peg.3148; -.
DR   EchoBASE; EB1068; -.
DR   eggNOG; COG1070; Bacteria.
DR   HOGENOM; CLU_009281_3_0_6; -.
DR   InParanoid; P09099; -.
DR   OMA; AACLDWA; -.
DR   OrthoDB; 9805576at2; -.
DR   PhylomeDB; P09099; -.
DR   BioCyc; EcoCyc:XYLULOKIN-MONOMER; -.
DR   BioCyc; MetaCyc:XYLULOKIN-MONOMER; -.
DR   BRENDA; 2.7.1.17; 2026.
DR   EvolutionaryTrace; P09099; -.
DR   PRO; PR:P09099; -.
DR   Proteomes; UP000000625; Chromosome.
DR   AbasyAtlas; P09099; -.
DR   GO; GO:0103020; F:1-deoxy-D-xylulose kinase activity; EXP:UniProtKB.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0004856; F:D-xylulokinase activity; IDA:EcoCyc.
DR   GO; GO:0016301; F:kinase activity; IBA:GO_Central.
DR   GO; GO:0042803; F:protein homodimerization activity; IDA:EcoCyc.
DR   GO; GO:0042843; P:D-xylose catabolic process; IMP:EcoCyc.
DR   GO; GO:0005998; P:xylulose catabolic process; IMP:EcoCyc.
DR   CDD; cd07808; ASKHA_NBD_FGGY_EcXK-like; 1.
DR   FunFam; 3.30.420.40:FF:000168; Xylulose kinase; 1.
DR   FunFam; 3.30.420.40:FF:000173; Xylulose kinase; 1.
DR   Gene3D; 3.30.420.40; -; 2.
DR   HAMAP; MF_02220; XylB; 1.
DR   InterPro; IPR043129; ATPase_NBD.
DR   InterPro; IPR000577; Carb_kinase_FGGY.
DR   InterPro; IPR018483; Carb_kinase_FGGY_CS.
DR   InterPro; IPR018485; FGGY_C.
DR   InterPro; IPR050406; FGGY_Carb_Kinase.
DR   InterPro; IPR018484; FGGY_N.
DR   InterPro; IPR006000; Xylulokinase.
DR   NCBIfam; TIGR01312; XylB; 1.
DR   NCBIfam; NF011601; xylB; 1.
DR   PANTHER; PTHR43095; SUGAR KINASE; 1.
DR   PANTHER; PTHR43095:SF6; XYLULOSE KINASE; 1.
DR   Pfam; PF02782; FGGY_C; 1.
DR   Pfam; PF00370; FGGY_N; 1.
DR   PIRSF; PIRSF000538; GlpK; 1.
DR   SUPFAM; SSF53067; Actin-like ATPase domain; 2.
DR   PROSITE; PS00933; FGGY_KINASES_1; 1.
DR   PROSITE; PS00445; FGGY_KINASES_2; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Allosteric enzyme; ATP-binding; Carbohydrate metabolism;
KW   Direct protein sequencing; Kinase; Nucleotide-binding; Reference proteome;
KW   Transferase; Xylose metabolism.
FT   CHAIN           1..484
FT                   /note="Xylulose kinase"
FT                   /id="PRO_0000059549"
FT   ACT_SITE        233
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02220,
FT                   ECO:0000305|PubMed:17123542"
FT   BINDING         77..78
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02220,
FT                   ECO:0000269|PubMed:17123542"
FT   SITE            6
FT                   /note="Important for activity"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02220,
FT                   ECO:0000305|PubMed:17123542"
FT   MUTAGEN         6
FT                   /note="D->A: Loss of activity."
FT                   /evidence="ECO:0000269|PubMed:17123542"
FT   MUTAGEN         233
FT                   /note="D->A: Loss of activity."
FT                   /evidence="ECO:0000269|PubMed:17123542"
FT   STRAND          2..7
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          9..17
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          23..30
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           45..62
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          70..75
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          80..83
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           102..111
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           115..119
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           128..138
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           140..143
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          148..150
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           152..161
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          165..167
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           168..172
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   TURN            173..175
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   TURN            179..182
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           186..190
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   TURN            191..193
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           196..198
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          201..203
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          207..211
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           214..220
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          226..228
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           233..241
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          249..262
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          271..273
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          275..278
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          285..291
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           294..304
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           310..316
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           317..319
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          328..333
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          345..353
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           358..381
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   TURN            382..384
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          390..394
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           395..397
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           400..410
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          414..418
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           424..436
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           442..445
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           447..450
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   STRAND          451..455
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           459..479
FT                   /evidence="ECO:0007829|PDB:2ITM"
FT   HELIX           480..483
FT                   /evidence="ECO:0007829|PDB:2ITM"
SQ   SEQUENCE   484 AA;  52618 MW;  8CC62CBD546AFCA0 CRC64;
     MYIGIDLGTS GVKVILLNEQ GEVVAAQTEK LTVSRPHPLW SEQDPEQWWQ ATDRAMKALG
     DQHSLQDVKA LGIAGQMHGA TLLDAQQRVL RPAILWNDGR CAQECTLLEA RVPQSRVITG
     NLMMPGFTAP KLLWVQRHEP EIFRQIDKVL LPKDYLRLRM TGEFASDMSD AAGTMWLDVA
     KRDWSDVMLQ ACDLSRDQMP ALYEGSEITG ALLPEVAKAW GMATVPVVAG GGDNAAGAVG
     VGMVDANQAM LSLGTSGVYF AVSEGFLSKP ESAVHSFCHA LPQRWHLMSV MLSAASCLDW
     AAKLTGLSNV PALIAAAQQA DESAEPVWFL PYLSGERTPH NNPQAKGVFF GLTHQHGPNE
     LARAVLEGVG YALADGMDVV HACGIKPQSV TLIGGGARSE YWRQMLADIS GQQLDYRTGG
     DVGPALGAAR LAQIAANPEK SLIELLPQLP LEQSHLPDAQ RYAAYQPRRE TFRRLYQQLL
     PLMA
//