Structural basis for a ribofuranosyl binding protein: Insights into the furanose specific transport
Ashima Bagaria
Department of Biology, Brookhaven National Laboratory, Upton, New York 11973
Search for more papers by this authorDesigan Kumaran
Department of Biology, Brookhaven National Laboratory, Upton, New York 11973
Search for more papers by this authorStephen K. Burley
Lilly Biotechnology Center, Eli Lilly and Company, San Diego, California 92121
Search for more papers by this authorCorresponding Author
Subramanyam Swaminathan
Department of Biology, Brookhaven National Laboratory, Upton, New York 11973
Biology Department, Brookhaven National Laboratory, Upton, NY 11973===Search for more papers by this authorAshima Bagaria
Department of Biology, Brookhaven National Laboratory, Upton, New York 11973
Search for more papers by this authorDesigan Kumaran
Department of Biology, Brookhaven National Laboratory, Upton, New York 11973
Search for more papers by this authorStephen K. Burley
Lilly Biotechnology Center, Eli Lilly and Company, San Diego, California 92121
Search for more papers by this authorCorresponding Author
Subramanyam Swaminathan
Department of Biology, Brookhaven National Laboratory, Upton, New York 11973
Biology Department, Brookhaven National Laboratory, Upton, NY 11973===Search for more papers by this author
Supporting Information
Additional Supporting Information may be found in the online version of this article.
Filename | Description |
---|---|
PROT_22965_sm_suppinfo.doc2 MB | Supporting Information |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
REFERENCES
- 1 Jones PM,George AM. The ABC transporter structure and mechanism: perspectives on recent research. Cell Mol Life Sci 2004; 61: 682–699.
- 2 Davidson AL,Dassa E,Orelle C,Chen J. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol Mol Biol Rev 2008; 72: 317–364.
- 3 Ordal GW. Bacterial chemotaxis: biochemistry of behavior in a single cell. Crit Rev Microbiol 1985; 12: 95–130.
- 4 Stewart RC,Dahlquist FW. Molecular components of bacterial chemotaxis. Chem Rev 1987; 87: 997–1025.
- 5 Stock J,Surette MG. Chemotaxis. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. Washington, DC: American Society for Microbiology Press; 1996. pp 1103–1129.
- 6 Duplay P,Szmelcman S,Bedouelle H,Hofnung M. Silent and functional changes in the periplasmic maltose-binding protein of Escherichia coli K12. I. Transport of maltose. J Mol Biol 1987; 194: 663–673.
- 7 Quiocho FA,Vyas NK. Novel stereospecificity of the L-arabinose-binding protein. Nature 1984; 310: 381–386.
- 8 Chaudhuri BN, Ko J, Park C, Jones TA, Mowbray SL. Structure of D-allose binding protein from Escherichia coli bound to D-allose at 1.8 A resolution. J Mol Biol 1999; 286, 1519–1531.
- 9 Zou JY,Flocco MM,Mowbray SL. The 1.7 A refined X-ray structure of the periplasmic glucose/galactose receptor from Salmonella typhimurium. J Mol Biol 1993; 233: 739–752.
- 10 Vyas NK,Vyas MN,Quiocho FA. Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. Science 1988; 242: 1290–1295.
- 11 Mowbray SL,Cole LB. 1.7 A X-ray structure of the periplasmic ribose receptor from Escherichia coli. J Mol Biol 1992; 225: 155–175.
- 12 Newcomer ME,Gilliland GL,Quiocho FA. L-Arabinose-binding protein-sugar complex at 2.4 A resolution. Stereochemistry and evidence for a structural change. J Biol Chem 1981; 256: 13213–13217.
- 13 Newcomer ME,Lewis BA,Quiocho FA. The radius of gyration of L-arabinose-binding protein decreases upon binding of ligand. J Biol Chem 1981; 256: 13218–13222.
- 14 Shilton BH,Flocco MM,Nilsson M,Mowbray SL. Conformational changes of three periplasmic receptors for bacterial chemotaxis and transport: the maltose-, glucose/galactose- and ribose-binding proteins. J Mol Biol 1996; 264: 350–363.
- 15 Bjorkman AJ,Mowbray SL. Multiple open forms of ribose-binding protein trace the path of its conformational change. J Mol Biol 1998; 279: 651–664.
- 16 Sharff AJ,Rodseth LE,Spurlino JC,Quiocho FA. Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis. Biochemistry 1992; 31: 10657–10663.
- 17 Galloway DR,Furlong CE. The role of ribose-binding protein in transport and chemotaxis in Escherichia coli K12. Arch Biochem Biophys 1977; 184: 496–504.
- 18 Otwinowski Z,Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 1997; 276: 307–326.
- 19 Schneider TR,Sheldrick GM. Substructure solution with SHELXD. Acta Crystallogr Sect D 2002; 58: 1772–1779.
- 20 De La Fortelle E,Bricogne G. Maximum-likelihood heavy atom parameter refinement in the MIR and MAD methods. Methods Enzymol 1997; 276: 472–493.
- 21 Abrahams JP,Leslie AG. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallogr Sect D 1996; 52: 30–42.
- 22 Langer G,Cohen SX,Lamzin VS,Perrakis A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 2008; 3: 1171–1179.
- 23 Emsley P,Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr Sect D 2004; 60: 2126–2132.
- 24 Murshudov GN,Vagin AA,Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr Sect D 1997; 53: 240–255.
- 25 Lin D,Manning NO,Jiang J,Abola EE,Stampf D,Prilusky J,Sussman JL. AutoDep: a web-based system for deposition and validation of macromolecular structural -information. Acta Crystallogr Sect D 2000; 56: 828–841.
- 26 Janin J,Miller S,Chothia C. Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol 1988; 204: 155–164.
- 27 Jones S,Thornton JM. Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol 1995; 63: 31–65.
- 28 Krissinel E,Henrick K. Inference of macromolecular assemblies from crystalline state. J Mol Biol 2007; 372: 774–797.
- 29 Aksamit RR,Koshland DE,Jr. Identification of the ribose binding protein as the receptor for ribose chemotaxis in Salmonella typhimurium. Biochemistry 1974; 13: 4473–4478.
- 30 Branden CI. Relation between structure and function of a/b proteins. Q Rev Biophys 1980; 13: 317–338.
- 31 Emekli U,Schneidman-Duhovny D,Wolfson HJ,Nussinov R,Haliloglu T. HingeProt: automated prediction of hinges in protein structures. Proteins 2008; 70: 1219–1227.
- 32 Horler RS,Muller A,Williamson DC,Potts JR,Wilson KS,Thomas GH. Furanose-specific sugar transport: characterization of a bacterial galactofuranose-binding protein. J Biol Chem 2009; 284: 31156–31163.
- 33 Chothia C,Lesk AM. Helix movements and the reconstruction of the haem pocket during the evolution of the cytochrome c family. J Mol Biol 1985; 182: 151–158.