Escherichia coli K-12 substr. MG1655 Enzyme: xylose isomerase

Gene: xylA Accession Numbers: EG11074 (EcoCyc), b3565, ECK3554

Regulation Summary Diagram: ?

Regulation summary diagram for xylA

Subunit composition of xylose isomerase = [XylA]4

Xylose isomerase catalyzes the first reaction in the catabolism of D-xylose [Wovcha83, Lawlis84, Rosenfeld84, Briggs84, Schellenberg84].

Two conserved histidine residues, H101 and H271, were shown to be essential for catalytic activity [Batt90]. The fluorescence of two conserved tryptophan residues, W49 and W188, is quenched during binding of xylose, and W49 was shown to be essential for catalytic activity [Jamieson92]. The presence of Mg2+, Mn2+ or Co2+ protects the enzyme from thermal denaturation [Epting05].

An amber mutation has been generated [Herring03].

The subunit composition has not been established experimentally.

Gene Citations: [Sumiya95, Song97]

Locations: cytosol

Map Position: [3,727,466 <- 3,728,788] (80.34 centisomes, 289°)
Length: 1323 bp / 440 aa

Molecular Weight of Polypeptide: 49.742 kD (from nucleotide sequence), 44 kD (experimental) [Schellenberg84 ]

pI: 6.1

Unification Links: ASAP:ABE-0011639 , CGSC:5 , DIP:DIP-11149N , EchoBASE:EB1067 , EcoGene:EG11074 , EcoliWiki:b3565 , Mint:MINT-1238504 , ModBase:P00944 , OU-Microarray:b3565 , PortEco:xylA , PR:PRO_000024240 , Pride:P00944 , Protein Model Portal:P00944 , RefSeq:NP_418022 , RegulonDB:EG11074 , SMR:P00944 , String:511145.b3565 , Swiss-Model:P00944 , UniProt:P00944

Relationship Links: InterPro:IN-FAMILY:IPR001998 , InterPro:IN-FAMILY:IPR013022 , InterPro:IN-FAMILY:IPR013452 , Pfam:IN-FAMILY:PF01261 , Prints:IN-FAMILY:PR00688 , Prosite:IN-FAMILY:PS51415

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for xylA

GO Terms:

Biological Process: GO:0042843 - D-xylose catabolic process Inferred from experiment [Briggs84]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0006098 - pentose-phosphate shunt Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0042732 - D-xylose metabolic process Inferred by computational analysis [UniProtGOA11a, GOA06]
Molecular Function: GO:0009045 - xylose isomerase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Wovcha83, Batt90]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for xylA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]
PMA carbon source test + D-xylose No 37 Aerobic     No [Bochner01]
PMA carbon source test + maltose No 37 Aerobic     No [Bochner01]
PMA carbon source test + maltotriose No 37 Aerobic     No [Bochner01]

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

Enzymatic reaction of: xylose isomerase

Synonyms: D-xylose ketol-isomerase

EC Number:

a D-xylopyranose <=> D-xylulose

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

This reaction is reversible.

Alternative Substrates for a D-xylopyranose: β-D-glucopyranose [Wovcha83 ]

In Pathways: xylose degradation I

The enzyme is also able to convert D-glucose to D-fructose under certain non-physiological conditions; the KM for glucose is 0.5 M [Wovcha83].

Cofactors or Prosthetic Groups: Mn2+ [Batt90]

T(opt): 70 °C [BRENDA14, Sapunova]

pH(opt): 7.5 [BRENDA14, Sapunova]

Sequence Features

Protein sequence of XylA with features indicated

Feature Class Location Citations Comment
Active-Site 101
[Batt90, UniProt11]
Active-Site 104
UniProt: Non-Experimental Qualifier: by similarity;
Sequence-Conflict 169
[Hou90, UniProt10a]
UniProt: (in Ref. 4; AAB20471);
Metal-Binding-Site 232
UniProt: Magnesium 1; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 268
UniProt: Magnesium 1; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 271
UniProt: Magnesium 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 296
UniProt: Magnesium 1; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 299
[Hou90, UniProt10a]
UniProt: (in Ref. 4; AAB20471);
Metal-Binding-Site 307
UniProt: Magnesium 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 309
UniProt: Magnesium 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 339
UniProt: Magnesium 1; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 342
[Hou90, UniProt10a]
UniProt: (in Ref. 4; AAB20471);
Sequence-Conflict 378
[Hou90, UniProt10a]
UniProt: (in Ref. 4; AAB20471);

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 b3565 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11074; 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

Batt90: Batt CA, Jamieson AC, Vandeyar MA (1990). "Identification of essential histidine residues in the active site of Escherichia coli xylose (glucose) isomerase." Proc Natl Acad Sci U S A 1990;87(2);618-22. PMID: 2405386

Bochner01: Bochner BR, Gadzinski P, Panomitros E (2001). "Phenotype microarrays for high-throughput phenotypic testing and assay of gene function." Genome Res 11(7);1246-55. PMID: 11435407

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Briggs84: Briggs KA, Lancashire WE, Hartley BS (1984). "Molecular cloning, DNA structure and expression of the Escherichia coli D-xylose isomerase." EMBO J 3(3);611-6. PMID: 6325179

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

Epting05: Epting KL, Vieille C, Zeikus JG, Kelly RM (2005). "Influence of divalent cations on the structural thermostability and thermal inactivation kinetics of class II xylose isomerases." FEBS J 272(6);1454-64. PMID: 15752361

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

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Herring03: Herring CD, Glasner JD, Blattner FR (2003). "Gene replacement without selection: regulated suppression of amber mutations in Escherichia coli." Gene 311;153-63. PMID: 12853150

Hou90: Hou YM, Zhang QJ, Wang SJ (1990). "Sequence analysis of D-xylose isomerase gene from Escherichia coli." Chin J Biotechnol 6(4);269-77. PMID: 2132127

Jamieson92: Jamieson AC, Batt CA (1992). "Fluorescent properties of the Escherichia coli D-xylose isomerase active site." Protein Eng 5(3);235-40. PMID: 1409543

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

Sapunova: Sapunova LI, Lobanok AG, Kazakevich IO, Shliakhotko EA, Evtushenkov AN "[Biosynthetic features and properties of xylose isomerases from Arthrobacter nicotianae, Escherichia coli, and Erwinia carotovota subsp. atroseptica]." Prikl Biokhim Mikrobiol 42(3);279-84. PMID: 16878542

Schellenberg84: Schellenberg GD, Sarthy A, Larson AE, Backer MP, Crabb JW, Lidstrom M, Hall BD, Furlong CE (1984). "Xylose isomerase from Escherichia coli. Characterization of the protein and the structural gene." J Biol Chem 259(11);6826-32. PMID: 6327696

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

Wovcha83: Wovcha MG, Steuerwald DL, Brooks KE (1983). "Amplification of D-xylose and D-glucose isomerase activities in Escherichia coli by gene cloning." Appl Environ Microbiol 1983;45(4);1402-4. PMID: 6344793

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
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