Major facilitator superfamily porters, LacY, FucP and XylE of escherichia coli appear to have evolved positionally dissimilar catalytic residues without rearrangement of 3-TMS repeat units

Journal of Molecular Microbiology and Biotechnology

Volumn 24, Issue 2, 2014, Pages 82-90

  Västermark, Åke ^a   Lunt, Bryan ^a   Saier, Milton ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Escherichia coli; FucP; LacY; Major facilitator superfamily; XylE

Indexed keywords

BACTERIAL PROTEIN; CARRIER PROTEIN; FUCOSE; FUCP PROTEIN; LACY PROTEIN; UNCLASSIFIED DRUG; XYLE PROTEIN; COTRANSPORTER; ESCHERICHIA COLI PROTEIN; FUCP PROTEIN, E COLI; GLUCOSE TRANSPORTER; LACY PROTEIN, E COLI; XYLE PROTEIN, E COLI; CARRIER PROTEINS AND BINDING PROTEINS; FUCP PORTER; LACY PORTER; OLIGOSACCHARIDE; XYLE PORTER;

3 TMS REPEAT UNIT; ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; ESCHERICHIA COLI; NONHUMAN; PEPTIDE MAPPING; PROTEIN CONFORMATION; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME ACTIVE SITE; ENZYMOLOGY; GENETICS; EVOLUTION;

ESCHERICHIA COLI;

CATALYTIC DOMAIN; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; MONOSACCHARIDE TRANSPORT PROTEINS; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SYMPORTERS;

EID: 84895701350     PISSN: 14641801     EISSN: 16602412     Source Type: Journal    
DOI: 10.1159/000358429     Document Type: Article

References (21)

1. Bailey TL, Elkan C: Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994; 2: 28-36.
2. Chang AB, Lin R, Keith Studley W, Tran CV, Saier MH Jr: Phylogeny as a guide to structure and function of membrane transport proteins. Mol Membr Biol 2004; 21: 171-181.
3. Chen JS, Reddy V, Chen JH, Shlykov MA, Zheng WH, Cho J, Yen MR, Saier MH Jr: Phylogenetic characterization of transport protein superfamilies: superiority of SuperFamilyTree programs over those based on multiple alignments. J Mol Microbiol Biotechnol 2011; 21: 83-96.
4. Dang S, Sun L, Huang Y, Lu F, Liu Y, Gong H, Wang J, Yan N: Structure of a fucose transporter in an outward-open conformation. Nature 2010; 467: 734-738.
5. Galil Z: Efficient algorithms for finding maximum matching in graphs. ACM Comput Surv 1986; 18: 23-38.
6. Guan L, Mirza O, Verner G, Iwata S, Kaback HR: Structural determination of wild-type lactose permease. Proc Natl Acad Sci USA 2007; 104: 15294-15298.
7. Henderson PJ: Studies of translocation catalysis. Biosci Rep 1991; 11: 477-453, discussion 534-538.
8. Henderson PJ, Maiden MC: Homologous sugar transport proteins in Escherichia coli and their relatives in both prokaryotes and eukaryotes. Philos Trans R Soc Lond B Biol Sci 1990; 326: 391-410.
9. Hvorup RN, Saier MH Jr: Sequence similarity between the channel-forming domains of voltage-gated ion channel proteins and the C-terminal domains of secondary carriers of the major facilitator superfamily. Microbiology 2002; 148(pt 12):3760-3762.
10. Madej MG, Dang S, Yan N, Kaback HR: Evolutionary mix-and-match with MFS transporters. Proc Natl Acad Sci USA 2013; 110: 5870-5874.
11. Marger MD, Saier MH Jr: A major superfamily of transmembrane facilitators that catalyse uniport, symport and antiport. Trends Biochem Sci 1993; 18: 13-20.
12. Pao SS, Paulsen IT, Saier MH Jr: Major facilitator superfamily. Microbiol Mol Biol Rev 1998; 62: 1-34.
13. Quistgaard EM, Löw C, Moberg P, Trésaugues L, Nordlund P: Structural basis for substrate transport in the GLUT-homology family of monosaccharide transporters. Nat Struct Mol Biol 2013; 20: 766-768.
14. Reddy VS, Saier MH Jr: BioV Suite: a collection of programs for the study of transport protein evolution. FEBS J 2012; 279: 2036-2046.
15. Reddy VS, Shlykov MA, Castillo R, Sun EI, Saier MH Jr: The major facilitator superfamily (MFS) revisited. FEBS J 2012; 279: 2022-2035.
16. Söding J: Protein homology detection by HMMHMM comparison. Bioinformatics 2005; 21: 951-960.
17. Sun L, Zeng X, Yan C, Sun X, Gong X, Rao Y, Yan N: Crystal structure of a bacterial homologue of glucose transporters GLUT1-4. Nature 2012; 490: 361-366.
18. von Heijne G: Membrane protein structure prediction: hydrophobicity analysis and the positive-inside rule. J Mol Biol 1992; 225: 487-494.
19. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ: Jalview version 2: a multiple sequence alignment editor and analysis workbench. Bioinformatics 2009; 25: 1189-1191.
20. Yen MR, Chen JS, Marquez JL, Sun EI, Saier MH: Multidrug resistance: phylogenetic characterization of superfamilies of secondary carriers that include drug exporters. Methods Mol Biol 2010; 637: 47-64.
21. Yen MR, Choi J, Saier MH Jr: Bioinformatic analyses of transmembrane transport: novel software for deducing protein phylogeny, topology, and evolution. J Mol Microbiol Biotechnol 2009; 17: 163-176.