Escherichia coli K-12 substr. MG1655 Enzyme: xylulokinase

Gene: xylB Accession Numbers: EG11075 (EcoCyc), b3564, ECK3553

Regulation Summary Diagram: ?

Regulation summary diagram for xylB

Subunit composition of xylulokinase = [XylB]2
         xylulokinase = XylB

Xylulokinase catalyzes the phosphorylation of D-xylulose, the second step in the xylose degradation pathway, producing D-xylulose-5-phosphate, an intermediate of the pentose phosphate pathway.

In the absence of substrate, xylulokinase has weak ATPase activity [Di07a]. Xylulokinase can also catalyze the phosphorylation of 1-deoxy-D-xylulose. This would allow a potential salvage pathway for generating 1-deoxy-D-xylulose 5-phosphate for use in the biosynthesis of terpenoids, thiamine and pyridoxal [Wungsintaweekul01].

The kinetic mechanism of the enzyme has been studied, suggesting a predominantly ordered reaction mechanism. The enzyme undergoes significant conformational changes upon binding of the substrate and of ATP. Two conserved aspartate residues, D6 and D233, were found to be essential for catalytic activity, and a catalytic mechanism has been proposed [Di07a].

Crystal structures of xylulokinase in the apo form and bound to D-xylulose have been determined at 2.7 and 2.1 Å resolution, respectively [Di07a].

Gene Citations: [Rosenfeld84, Sumiya95, Song97]

Locations: cytosol

Map Position: [3,725,940 <- 3,727,394] (80.31 centisomes, 289°)
Length: 1455 bp / 484 aa

Molecular Weight of Polypeptide: 52.618 kD (from nucleotide sequence)

Molecular Weight of Multimer: 110 kD (experimental) [Di07a]

Unification Links: ASAP:ABE-0011637 , CGSC:4 , EchoBASE:EB1068 , EcoGene:EG11075 , EcoliWiki:b3564 , ModBase:P09099 , OU-Microarray:b3564 , PortEco:xylB , Pride:P09099 , Protein Model Portal:P09099 , RefSeq:NP_418021 , RegulonDB:EG11075 , SMR:P09099 , String:511145.b3564 , UniProt:P09099

Relationship Links: InterPro:IN-FAMILY:IPR006000 , InterPro:IN-FAMILY:IPR018483 , InterPro:IN-FAMILY:IPR018484 , InterPro:IN-FAMILY:IPR018485 , PDB:Structure:2ITM , PDB:Structure:2NLX , Pfam:IN-FAMILY:PF00370 , Pfam:IN-FAMILY:PF02782 , Prosite:IN-FAMILY:PS00445 , Prosite:IN-FAMILY:PS00933

In Paralogous Gene Group: 21 (7 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for xylB

GO Terms:

Biological Process: GO:0005998 - xylulose catabolic process Inferred from experiment [Rosenfeld84]
GO:0042843 - D-xylose catabolic process Inferred from experiment [Lawlis84]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0005997 - xylulose metabolic process Inferred by computational analysis [GOA01a]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a]
GO:0042732 - D-xylose metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0046835 - carbohydrate phosphorylation Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0004856 - xylulokinase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Di07a]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016773 - phosphotransferase activity, alcohol group as acceptor Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [Gaudet10]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for xylB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]
Yes [Feist07, Comment 3]

Created 09-Jan-2007 by Keseler I , SRI International
Last-Curated ? 09-Jan-2007 by Keseler I , SRI International

Enzymatic reaction of: xylulokinase

Synonyms: xylulose kinase

EC Number:

D-xylulose + ATP <=> D-xylulose 5-phosphate + ADP + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: xylose degradation I

D-xylulose is strongly preferred over alternative substrates; the catalytic efficiency with substrates such as D-ribulose and D-arabitol is 50- to 1300-fold lower [Di07a].

Inhibitors (Competitive): 5-fluoro-xylulose [Di07a] , AMPPNP [Di07a]

Kinetic Parameters:

Km (μM)

Enzymatic reaction of: 1-deoxy-D-xylulose kinase (xylulokinase)

EC Number: 2.7.1.-

ATP + 1-deoxy-D-xylulose <=> 1-deoxy-D-xylulose 5-phosphate + ADP + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

The rate of phosphorylation of 1-deoxy-D-xylulose is 32-fold lower than the rate of phosphorylation of D-xylulose [Wungsintaweekul01].

Cofactors or Prosthetic Groups: Mg2+ [Wungsintaweekul01]

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3564 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11075; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Di07a: Di Luccio E, Petschacher B, Voegtli J, Chou HT, Stahlberg H, Nidetzky B, Wilson DK (2007). "Structural and Kinetic Studies of Induced Fit in Xylulose Kinase from Escherichia coli." J Mol Biol 365(3);783-98. PMID: 17123542

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lawlis84: Lawlis VB, Dennis MS, Chen EY, Smith DH, Henner DJ (1984). "Cloning and sequencing of the xylose isomerase and xylulose kinase genes of Escherichia coli." Appl Environ Microbiol 47(1);15-21. PMID: 6320721

Rosenfeld84: Rosenfeld SA, Stevis PE, Ho NW (1984). "Cloning and characterization of the xyl genes from Escherichia coli." Mol Gen Genet 1984;194(3);410-5. PMID: 6330500

Song97: Song S, Park C (1997). "Organization and regulation of the D-xylose operons in Escherichia coli K-12: XylR acts as a transcriptional activator." J Bacteriol 1997;179(22);7025-32. PMID: 9371449

Sumiya95: Sumiya M, Davis EO, Packman LC, McDonald TP, Henderson PJ (1995). "Molecular genetics of a receptor protein for D-xylose, encoded by the gene xylF, in Escherichia coli." Receptors Channels 1995;3(2);117-28. PMID: 8581399

Tritsch04: Tritsch D, Hemmerlin A, Rohmer M, Bach TJ (2004). "A sensitive radiometric assay to measure D-xylulose kinase activity." J Biochem Biophys Methods 58(1);75-83. PMID: 14597191

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wungsintaweekul01: Wungsintaweekul J, Herz S, Hecht S, Eisenreich W, Feicht R, Rohdich F, Bacher A, Zenk MH (2001). "Phosphorylation of 1-deoxy-D-xylulose by D-xylulokinase of Escherichia coli." Eur J Biochem 2001;268(2);310-6. PMID: 11168365

Other References Related to Gene Regulation

Desai09: Desai TA, Rao CV (2009). "Regulation of arabinose and xylose metabolism in Escherichia coli." Appl Environ Microbiol. PMID: 20023096

Laikova01: Laikova ON, Mironov AA, Gelfand MS (2001). "Computational analysis of the transcriptional regulation of pentose utilization systems in the gamma subdivision of Proteobacteria." FEMS Microbiol Lett 205(2);315-22. PMID: 11750821

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Wed Oct 7, 2015, biocyc12.