XYLB_ECOLI
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 03-AUG-2022, entry version 152.
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; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC 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 (2.10 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH
RP D-XYLULOSE, FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, ACTIVE SITE, AND MUTAGENESIS OF
RP 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=ATP + D-xylulose = ADP + D-xylulose 5-phosphate + 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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
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_SSZK01000041.1.
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 PDBsum; 2ITM; -.
DR PDBsum; 2NLX; -.
DR AlphaFoldDB; P09099; -.
DR SMR; P09099; -.
DR BioGRID; 4262539; 11.
DR IntAct; P09099; 1.
DR STRING; 511145.b3564; -.
DR jPOST; P09099; -.
DR PaxDb; P09099; -.
DR PRIDE; P09099; -.
DR EnsemblBacteria; AAC76588; AAC76588; b3564.
DR EnsemblBacteria; BAE77729; BAE77729; BAE77729.
DR GeneID; 948133; -.
DR KEGG; ecj:JW3536; -.
DR KEGG; eco:b3564; -.
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; WHVMGVT; -.
DR PhylomeDB; P09099; -.
DR BioCyc; EcoCyc:XYLULOKIN-MON; -.
DR BioCyc; MetaCyc:XYLULOKIN-MON; -.
DR BRENDA; 2.7.1.17; 2026.
DR EvolutionaryTrace; P09099; -.
DR PRO; PR:P09099; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0103020; F:1-deoxy-D-xylulose kinase activity; IEA:RHEA.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004856; F:xylulokinase 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 HAMAP; MF_02220; XylB; 1.
DR InterPro; IPR043129; ATPase_NBD.
DR InterPro; IPR000577; Carb_kinase_FGGY.
DR InterPro; IPR018485; Carb_kinase_FGGY_C.
DR InterPro; IPR018483; Carb_kinase_FGGY_CS.
DR InterPro; IPR018484; Carb_kinase_FGGY_N.
DR InterPro; IPR006000; Xylulokinase.
DR Pfam; PF02782; FGGY_C; 1.
DR Pfam; PF00370; FGGY_N; 1.
DR PIRSF; PIRSF000538; GlpK; 1.
DR SUPFAM; SSF53067; SSF53067; 2.
DR TIGRFAMs; TIGR01312; XylB; 1.
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..219
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 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
