Escherichia coli K-12 substr. MG1655 Transporter: xylose:H+ symporter

Gene: xylE Accession Numbers: EG11076 (EcoCyc), b4031, ECK4023

Synonyms: xylose MFS transporter

Regulation Summary Diagram: ?

Regulation summary diagram for xylE

XylE is a D-xylose/proton symporter, one of two systems in E. coli K-12 responsible for the uptake of D-xylose - the other being the ATP-dependent ABC transporter XylFGH. The cloned xylE gene has been shown to complement xylE mutants in vivo [Davis87]. XylE-mediated transport in whole cells is inhibited by protonophores and elicits an alkaline pH change [Lam80]. Experiments using xylE and xylF mutants have established that XylE has a Km of 63-169 μM for D-xylose [Sumiya95].

Crystal structures of XylE bound to the ligands D-xylose, D-glucose and the chemically sysnthesized glucose derivative, 6-bromo-6-deoxy-D-glucose have been obtained at 2.6 - 2.9 Å. Structures were captured in an outward facing conformation. XylE contains 12 transmembrane (TM) helices organised into two distinct domains with amino and carboxy termini located on the cytosolic side of the membrane. XylE also contains an intracellular domain consisting of 4 helices - 3 of these connect the TM domains, the fourth is located at the C-terminal end of the protein [Sun12a]. Crystal structures of XylE in inward opening conformations are also available [Quistgaard13, Quistgaard13a].

D-glucose is a strong inhibitor of xylose transport in in vitro sugar competition assays. Other hexose and pentose sugars (D-galactose, L-fucose, L-arabinose, D-mannose and L-rhamnose) had no effect [Sun12a]. D-glucose does not induce the XylE transport system [Lam80].

XylE mutants with neutral replacements at Asp27 (XylE D27N and XylE D27A) do not catalyse D-xylose:H+ symport although binding and counterflow activity remain similar to the wild-type suggesting that Asp27 is involved in proton transport. A XylE double mutant Q175I / L297F transports D-glucose although at a lower level than D-xylose [Madej14].

XylE is a member of the major facilitator superfamily (MFS) of transporters [Griffith92]. The xylE gene probably constitutes a monocistronic operon whose expression is inducible by D-xylose. Imported xylose is catabolised to xylulose-5-phosphate by the action of the XylA and XylB enzymes.

Locations: inner membrane

Map Position: [4,238,802 <- 4,240,277] (91.36 centisomes, 329°)
Length: 1476 bp / 491 aa

Molecular Weight of Polypeptide: 53.608 kD (from nucleotide sequence), 39.0 kD (experimental) [Maiden87 ]

Unification Links: ASAP:ABE-0013189 , CGSC:17776 , EchoBASE:EB1069 , EcoGene:EG11076 , EcoliWiki:b4031 , ModBase:P0AGF4 , OU-Microarray:b4031 , PortEco:xylE , PR:PRO_000024241 , Pride:P0AGF4 , Protein Model Portal:P0AGF4 , RefSeq:NP_418455 , RegulonDB:EG11076 , SMR:P0AGF4 , String:511145.b4031 , UniProt:P0AGF4

Relationship Links: InterPro:IN-FAMILY:IPR003663 , InterPro:IN-FAMILY:IPR005828 , InterPro:IN-FAMILY:IPR005829 , InterPro:IN-FAMILY:IPR020846 , PDB:Structure:4GBY , PDB:Structure:4GBZ , PDB:Structure:4GC0 , PDB:Structure:4JA3 , PDB:Structure:4JA4 , PDB:Structure:4QIQ , Pfam:IN-FAMILY:PF00083 , Prints:IN-FAMILY:PR00171 , Prosite:IN-FAMILY:PS00216 , Prosite:IN-FAMILY:PS00217 , Prosite:IN-FAMILY:PS50850

In Paralogous Gene Group: 17 (37 members) , 566 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0015753 - D-xylose transport Inferred from experiment [Davis87, Lam80, Sun12a]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11]
GO:0008643 - carbohydrate transport Inferred by computational analysis [UniProtGOA11]
GO:0055085 - transmembrane transport Inferred by computational analysis [GOA01]
Molecular Function: GO:0015519 - D-xylose:proton symporter activity Inferred from experiment [Lam80, Sun12a]
GO:0005215 - transporter activity Inferred by computational analysis [GOA01]
GO:0015293 - symporter activity Inferred by computational analysis [UniProtGOA11]
GO:0022857 - transmembrane transporter activity Inferred by computational analysis [GOA01]
GO:0022891 - substrate-specific transmembrane transporter activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
GO:0005887 - integral component of plasma membrane Inferred from experiment Inferred by computational analysis [Davis87, Sun12a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11, GOA01]

MultiFun Terms: cell structure membrane
metabolism carbon utilization carbon compounds
transport Electrochemical potential driven transporters Porters (Uni-, Sym- and Antiporters)

Essentiality data for xylE 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]

Enzymatic reaction of: transport of D-xylose (xylose:H+ symporter)

Transport reaction diagram for transport of D-xylose

Inhibitors (Competitive): D-glucose [Sun12a]

Sequence Features

Protein sequence of xylose:H+ symporter with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 10 -> 32
UniProt: Helical; Name=1.
Mutagenesis-Variant 24
[Sun12a, UniProt14]
UniProt: Decreases xylose transport.
Amino-Acid-Site 27
implicated in proton binding
Transmembrane-Region 59 -> 79
UniProt: Helical; Name=2.
Sequence-Conflict 64
[Francoz88, UniProt10a]
UniProt: (in Ref. 6; CAA29863);
Mutagenesis-Variant 83
[Sun12a, UniProt14]
UniProt: Abolishes xylose transport.
Transmembrane-Region 85 -> 105
UniProt: Helical; Name=3.
Transmembrane-Region 129 -> 150
UniProt: Helical; Name=4.
Mutagenesis-Variant 133
[UniProt14, Sun12a, UniProt14]
R → C, H or L: Abolishes xylose transport.
Mutagenesis-Variant 153
[Sun12a, UniProt14]
UniProt: Abolishes xylose transport.
Mutagenesis-Variant 160
[Sun12a, UniProt14]
UniProt: Abolishes xylose transport.
Transmembrane-Region 163 -> 183
UniProt: Helical; Name=5.
Amino-Acid-Sites-That-Bind 168
UniProt: Monosaccharide.
Mutagenesis-Variant 168
[Sun12a, UniProt14]
UniProt: Abolishes xylose transport.
Transmembrane-Region 201 -> 221
UniProt: Helical; Name=6;; Non-Experimental Qualifier: potential;
Transmembrane-Region 277 -> 299
UniProt: Helical; Name=7.
Mutagenesis-Variant 288
[Sun12a, UniProt14]
UniProt: Abolishes xylose transport.
Protein-Segment 288 -> 294
UniProt: Monosaccharide binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 289
[Sun12a, UniProt14]
UniProt: Strongly decreases xylose transport.
Mutagenesis-Variant 294
[Sun12a, UniProt14]
UniProt: Abolishes xylose transport.
Mutagenesis-Variant 298
[Sun12a, UniProt14]
UniProt: Abolishes xylose transport.
Transmembrane-Region 313 -> 334
UniProt: Helical; Name=8.
Mutagenesis-Variant 325
[Sun12a, UniProt14]
UniProt: No effect on xylose transport.
Mutagenesis-Variant 340
[Sun12a, UniProt14]
UniProt: Abolishes xylose transport.
Mutagenesis-Variant 341
[Sun12a, UniProt14]
R → A or W: Abolishes xylose transport.
Transmembrane-Region 344 -> 364
UniProt: Helical; Name=9;; Non-Experimental Qualifier: potential;
Transmembrane-Region 370 -> 390
UniProt: Helical; Name=10;; Non-Experimental Qualifier: potential;
Amino-Acid-Sites-That-Bind 392
UniProt: Monosaccharide.
Mutagenesis-Variant 392
[Sun12a, UniProt14]
UniProt: Abolishes xylose transport.
Mutagenesis-Variant 397
[Sun12a, UniProt14]
UniProt: Abolishes xylose transport.
Mutagenesis-Variant 404
[Sun12a, UniProt14]
UniProt: Strongly decreases xylose transport.
Transmembrane-Region 408 -> 428
UniProt: Helical; Name=11;; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 415
UniProt: Strongly decreases xylose transport.
Amino-Acid-Sites-That-Bind 415
UniProt: Monosaccharide.
Mutagenesis-Variant 416
[Sun12a, UniProt14]
UniProt: Strongly decreases xylose transport.
Transmembrane-Region 443 -> 463
UniProt: Helical; Name=12;; Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b4031 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11076; 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

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

Davis87: Davis EO, Henderson PJ (1987). "The cloning and DNA sequence of the gene xylE for xylose-proton symport in Escherichia coli K12." J Biol Chem 1987;262(29);13928-32. PMID: 2820984

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

Francoz88: Francoz E, Dassa E (1988). "3' end of the malEFG operon in E.coli: localization of the transcription termination site." Nucleic Acids Res 1988;16(9);4097-109. PMID: 2836810

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

Griffith92: Griffith JK, Baker ME, Rouch DA, Page MG, Skurray RA, Paulsen IT, Chater KF, Baldwin SA, Henderson PJ (1992). "Membrane transport proteins: implications of sequence comparisons." Curr Opin Cell Biol 1992;4(4);684-95. PMID: 1419050

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

Lam80: Lam VM, Daruwalla KR, Henderson PJ, Jones-Mortimer MC (1980). "Proton-linked D-xylose transport in Escherichia coli." J Bacteriol 1980;143(1);396-402. PMID: 6995439

Madej14: Madej MG, Sun L, Yan N, Kaback HR (2014). "Functional architecture of MFS D-glucose transporters." Proc Natl Acad Sci U S A 111(7);E719-27. PMID: 24550316

Maiden87: Maiden MC, Davis EO, Baldwin SA, Moore DC, Henderson PJ (1987). "Mammalian and bacterial sugar transport proteins are homologous." Nature 325(6105);641-3. PMID: 3543693

Quistgaard13: Quistgaard EM, Low C, Moberg P, Tresaugues L, Nordlund P (2013). "Structural basis for substrate transport in the GLUT-homology family of monosaccharide transporters." Nat Struct Mol Biol 20(6);766-8. PMID: 23624861

Quistgaard13a: Quistgaard EM, Low C, Moberg P, Nordlund P (2013). "Metal-mediated crystallization of the xylose transporter XylE from Escherichia coli in three different crystal forms." J Struct Biol. PMID: 24060988

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

Sun12a: Sun L, Zeng X, Yan C, Sun X, Gong X, Rao Y, Yan N (2012). "Crystal structure of a bacterial homologue of glucose transporters GLUT1-4." Nature 490(7420);361-6. PMID: 23075985

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.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

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

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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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