Crystal structure of the bacterial nucleoside transporter Tsx

EMBO Journal

Volumn 23, Issue 16, 2004, Pages 3187-3195

  Ye, Jiqing ^a   Van Den Berg, Bert ^a,b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

Binding site; Crystal structure; ENT; Nucleoside transporter; Outer membrane protein

Indexed keywords

NUCLEOSIDE TRANSPORTER; OUTER MEMBRANE PROTEIN;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; DNA FLANKING REGION; ENZYME SPECIFICITY; ESCHERICHIA COLI; GRAM NEGATIVE BACTERIUM; HYDROGEN BOND; MEMBRANE TRANSPORT; NONHUMAN; NUCLEOSIDE TRANSPORT; OUTER MEMBRANE; PRIORITY JOURNAL; RESIDUE ANALYSIS; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; BACTERIAL OUTER MEMBRANE PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EUKARYOTIC CELLS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEOSIDE TRANSPORT PROTEINS; NUCLEOSIDES; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, VIRUS; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 4444258925     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.emboj.7600330     Document Type: Article

References (42)

1. Abramson J, Smirnova I, Kasho V, Verner G, Iwata S, Kaback HR (2003) The lactose permease of Escherichia coli: overall structure, the sugar-binding site and the alternating access model for transport. FEBS Lett 555: 96-101
2. Acimovic Y, Coe IR (2002) Molecular evolution of the equilibrative nucleoside transporter family: identification of novel family members in prokaryotes and eukaryotes. Mol Biol Evol 19: 2199-2210
3. Benz R, Schmid A, Maier C, Bremer E (1988) Characterization of the nucleoside-binding site inside the Tsx channel of Escherichia coli outer membrane. Reconstitution experiments with lipid bilayer membranes. Eur J Biochem 176: 699-705
4. Benz R, Schmid A, Vos-Scheperkeuter GH (1987) Mechanism of sugar transport through the sugar-specific LamB channel of Escherichia coli outer membrane. J Membr Biol 100: 21-29
5. Birch RG, Patil SS (1985) Preliminary characterization of an antibiotic produced by Xanthomonas albilineans which inhibits DNA synthesis in Eschenchia coli. J Gen Microbiol 131 (Part 5): 1069-1075
6. Birch RG, Pemberton JM, Basnayake WV (1990) Stable albicidin resistance in Escherichia coli involves an altered outer-membrane nucleoside uptake system. J Gen Microbiol 136 (Part 1): 51-58
7. Braun V, Braun M (2002) Active transport of iron and siderophore antibiotics. Curr Opin Microbiol 5: 194-201
8. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54 (Part 5): 905-921
9. Carson M (1991) Ribbons 2.0. J Appl Crystallogr 24: 958-961
10. Clarke TE, Tari LW, Vogel HJ (2001) Structural biology of bacterial iron uptake systems. Curr Top Med Chem 1: 7-30
11. Craig JE, Zhang Y, Gallagher MP (1994) Cloning of the nupC gene of Escherichia coli encoding a nucleoside transport system, and identification of an adjacent insertion element, IS 186. Mol Microbiol 11: 1159-1168
12. Dutzler R, Schirmer T, Karplus M, Fischer S (2002) Translocation mechanism of long sugar chains across the maltoporin membrane channel. Structure (Camb) 10: 1273-1284
13. Ferguson AD, Deisenhofer J (2004) Metal import through microbial membranes. Cell 116: 15-24
14. Forst D, Welte W, Wacker T, Diederichs K (1998) Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose. Nat Struct Biol 5: 37-46
15. Fsihi H, Kottwitz B, Bremer E (1993) Single amino acid substitutions affecting the substrate specificity of the Escherichia coli K-12 nucleoside-specific Tsx channel. J Biol Chem 268: 17495-17503
16. Guzman LM, Belin D, Carson MJ, Beckwith J (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol 177: 4121-4130
17. Hantke K (1976) Phage T6-colicin K receptor and nucleoside transport in Escherichia coli. FEBS Lett 70: 109-112
18. Hardesty C, Ferran C, DiRienzo JM (1991) Plasmid-mediated sucrose metabolism in Escherichia coli: characterization of scrY, the structural gene for a phosphoenolpyruvate-dependent sucrose phosphotransferase system outer membrane porin. J Bacteriol 173: 449-456
19. Jones TA, Zou JY, Cowan SW, Kjeldgaard M (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 47 (Part 2): 110-119
20. Kantardjieff KA, Rupp B (2003) Matthews coefficient probabilities: improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Prot Science 12: 1865-1871
21. Luckey M, Nikaido H (1980) Specificity of diffusion channels produced by lambda phage receptor protein of Escherichia coli. Proc Natl Acad Sci USA 77: 167-171
22. Maier C, Bremer E, Schmid A, Benz R (1988) Pore-forming activity of the Tsx protein from the outer membrane of Escherichia coli. Demonstration of a nucleoside-specific binding site. J Biol Chem 263: 2493-2499
23. Manning PA, Reeves P (1976) Outer membrane of Escherichia coli K-12: TSX mutants (resistant to bacteriophage T6 and colicin K) lack an outer membrane protein. Biochem Biophys Res Commun 71: 466-471
24. McKeown M, Kahn M, Hanawalt P (1976) Thymidine uptake and utilization in Escherichia coli: a new gene controlling nucleoside transport. J Bacteriol 126: 814-822
25. Munch-Petersen A, Jensen N (1990) Analysis of the regulatory region of the Escherichia coli nupG gene, encoding a nucleoside-transport protein. Eur J Biochem 190: 547-551
26. Munch-Petersen A, Mygind B, Nicolaisen A, Pihl NJ (1979) Nucleoside transport in cells and membrane vesicles from Escherichia coli K12. J Biol Chem 254: 3730-3737
27. Nieweg A, Bremer E (1997) The nucleoside-specific Tsx channel from the outer membrane of Salmonella typhimurium, Klebsiella pneumoniae and Enterobacter aerogenes: functional characterization and DNA sequence analysis of the tsx genes. Microbiology 143 (Part 2): 603-615
28. Nikaido H (1994) Porins and specific diffusion channels in bacterial outer membranes. J Biol Chem 269: 3905-3908
29. Nikaido H (2003) Molecular basis of bacterial outer membrane permeability revisited. Microbiol Mol Biol Rev 67: 593-656
30. Norholm MH, Dandanell G (2001) Specificity and topology of the Escherichia coli xanthosine permease, a representative of the NHS subfamily of the major facilitator superfamily. J Bacteriol 183: 4900-4904
31. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307-326
32. Postle K, Kadner RJ (2003) Touch and go: tying TonB to transport. Mol Microbiol 49: 869-882
33. Saenger W (1983) Principles of Nucleic Acid Structure. New York: Springer-Verlag Inc
34. Schirmer T, Keller TA, Wang YF, Rosenbusch JP (1995) Structural basis for sugar translocation through maltoporin channels at 3.1 A resolution. Science 267: 512-514
35. Schwarz G, Danelon C, Winterhalter M (2003) On translocation through a membrane channel via an internal binding site: kinetics and voltage dependence. Biophys J 84: 2990-2998
36. Terwilliger TC (2003) SOLVE and RESOLVE: automated structure solution and density modification. Methods Enzymol 374: 22-37
37. Terwilliger TC, Berendzen J (1999) Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 55 (Part 4): 849-861
38. Trias J, Nikaido H (1990) Protein D2 channel of the Pseudomonas aeruginosa outer membrane has a binding site for basic amino acids and peptides. J Biol Chem 265: 15680-15684
39. Trias J, Rosenberg EY, Nikaido H (1988) Specificity of the glucose channel formed by protein D1 of Pseudomonas aeruginosa. Biochim Biophys Acta 938: 493-496
40. van Alphen W, van Seim N, Lugtenberg B (1978) Pores in the outer membrane of Escherichia coli K12: involvement of proteins b and e in the functioning of pores for nucleotides. Mol Gen Genet 159: 75-83
41. Van Duyne GD, Standaert RF, Karplus PA, Schreiber SL, Clardy J (1993) Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J Mol Biol 229: 105-124
42. Westh Hansen SE, Jensen N, Munch-Petersen A (1987) Studies on the sequence and structure of the Escherichia coli K-12 nupG gene, encoding a nucleoside-transport system. Eur J Biochem 168: 385-391