Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for α-keto acid binding

BMC Structural Biology

Volumn 7, Issue , 2007, Pages

  Gonin, Sophie ^a   Arnoux, Pascal ^a   Pierru, Bénédicte ^a   Lavergne, Jérôme ^a   Alonso, Béatrice ^b   Sabaty, Monique ^a   Pignol, David ^a  

^a IRFM   (France)

^b CEA Marcoule   (France)

Author keywords

[No Author keywords available]

Indexed keywords

2 OXOACID; BINDING PROTEIN; CARRIER PROTEIN; CATION; DIMER; PYRUVATE SODIUM; TRAP TRANSPORTER ALPHA KETO ACID BINDING P SUBUNIT; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING SITE; CRYSTAL STRUCTURE; PROTEIN BINDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

BACTERIAL PROTEINS; BIOLOGICAL TRANSPORT; CARRIER PROTEINS; CATIONS; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; KETO ACIDS; MEMBRANE TRANSPORT PROTEINS; PROTEIN STRUCTURE, SECONDARY; RHODOBACTER SPHAEROIDES; RNA-BINDING PROTEINS; TRANSCRIPTION FACTORS;

BACTERIA (MICROORGANISMS); DIONAEA; RHODOBACTER SPHAEROIDES;

EID: 34047164005     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-7-11     Document Type: Article

References (42)

1. TCDB: the Transporter Classification Database for membrane transport protein analyses and information. MH Saier Jr. CV Tran RD Barabote, Nucleic Acids Res 2006 34 Database issue D181 6 16381841 10.1093/nar/gkj001
2. Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history. K Fukami-Kobayashi Y Tateno K Nishikawa, J Mol Biol 1999 286 1 279 290 10.1006/jmbi.1998.2454 9931266
3. Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis: variation of common themes. FA Quiocho PS Ledvina, Mol Microbiol 1996 20 1 17 25 10.1111/j.1365-2958.1996.tb02484.x 8861200
4. The ATP switch model for ABC transporters. CF Higgins KJ Linton, Nat Struct Mol Biol 2004 11 10 918 926 10.1038/nsmb836 15452563
5. TRAP transporters: a new family of periplasmic solute transport systems encoded by the dctPQM genes of Rhodobacter capsulatus and by homologs in diverse gram-negative bacteria. JA Forward MC Behrendt NR Wyborn R Cross DJ Kelly, J Bacteriol 1997 179 17 5482 5493 9287004
6. TRAP transporters: an ancient family of extracytoplasmic solute-receptor-dependent secondary active transporters. R Rabus DL Jack DJ Kelly MH Saier Jr., Microbiology 1999 145 ( Pt 12) 3431 3445 10627041
7. Transport of C(4)-dicarboxylates in Wolinella succinogenes. R Ullmann R Gross J Simon G Unden A Kroger, J Bacteriol 2000 182 20 5757 5764 11004174 10.1128/JB.182.20.5757-5764.2000
8. New type of osmoregulated solute transporter identified in halophilic members of the bacteria domain: TRAP transporter TeaABC mediates uptake of ectoine and hydroxyectoine in Halomonas elongata DSM 2581(T). K Grammann A Volke HJ Kunte, J Bacteriol 2002 184 11 3078 3085 12003950 10.1128/JB.184.11.3078- 3085.2002
9. Identification of genes encoding amino acid permeases by inactivation of selected ORFs from the Synechocystis genomic sequence. MJ Quintero ML Montesinos A Herrero E Flores, Genome Res 2001 11 12 2034 2040 11731493 10.1101/gr.196301
10. Functional characterization of the Escherichia coli K-12 yiaMNO transport protein genes. TH Plantinga C Van Der Does J Badia J Aguilar WN Konings AJ Driessen, Mol Membr Biol 2004 21 1 51 57 10.1080/09687680310001607369 14668138
11. Sialic acid transport in Haemophilus influenzae is essential for lipopolysaccharide sialylation and serum resistance and is dependent on a novel tripartite ATP-independent periplasmic transporter. E Severi G Randle P Kivlin K Whitfield R Young R Moxon D Kelly D Hood GH Thomas, Mol Microbiol 2005 58 4 1173 1185 10.1111/j.1365-2958.2005.04901.x 16262798
12. C4-dicarboxylate carriers and sensors in bacteria. IG Janausch E Zientz QH Tran A Kroger G Unden, Biochim Biophys Acta 2002 1553 1-2 39 56 10.1016/S0005-2728(01)00233-X 11803016
13. Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid-binding virulence factor from Haemophilus influenzae. A Muller E Severi C Mulligan AG Watts DJ Kelly KS Wilson AJ Wilkinson GH Thomas, J Biol Chem 2006 281 31 22212 22222 10.1074/jbc.M603463200 16702222
14. Cloning, nucleotide sequence, and overexpression of smoS, a component of a novel operon encoding an ABC transporter and polyol dehydrogenases of Rhodobacter sphaeroides Si4. MA Stein A Schafer F Giffhorn, J Bacteriol 1997 179 20 6335 6340 9335280
15. Novel ligands for the extracellular solute receptors of two bacterial TRAP transporters. GH Thomas T Southworth MR Leon-Kempis A Leech DJ Kelly, Microbiology 2006 152 Pt 1 187 198 10.1099/mic.0.28334-0 16385129
16. Genetic and biochemical evidence for the involvement of a molybdenum-dependent enzyme in one of the selenite reduction pathways of Rhodobacter sphaeroides f. sp. denitrificans IL106. B Pierru S Grosse D Pignol M Sabaty, Appl Environ Microbiol 2006 72 5 3147 3153 16672451 10.1128/AEM.72.5.3147-3153.2006
17. ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces. RP Saha RP Bahadur A Pal S Mandal P Chakrabarti, BMC Struct Biol 2006 6 11 16759379 10.1186/1472-6807-6-11
18. Protein structure comparison by alignment of distance matrices. L Holm C Sander, J Mol Biol 1993 233 1 123 138 10.1006/jmbi.1993.1489 8377180
19. Cation-pi interactions as determinants for binding of the compatible solutes glycine betaine and proline betaine by the periplasmic ligand-binding protein ProX from Escherichia coli. A Schiefner J Breed L Bosser S Kneip J Gade G Holtmann K Diederichs W Welte E Bremer, J Biol Chem 2004 279 7 5588 5596 10.1074/jbc.M309771200 14612446
20. Probing the function, conformational plasticity, and dimer-dimer contacts of the GluR2 ligand-binding core: studies of 5-substituted willardiines and GluR2 S1S2 in the crystal. R Jin E Gouaux, Biochemistry 2003 42 18 5201 5213 10.1021/bi020632t 12731861
21. Crystal structure of ATP phosphoribosyltransferase from Micobacterium tuberculosis. Y Cho V Sharma JC Sacchettini, J Biol Chem 2003 278 10 8333 8339 10.1074/jbc.M212124200 12511575
22. Identification of protein oligomerization states by analysis of interface conservation. AH Elcock JA McCammon, Proc Natl Acad Sci U S A 2001 98 6 2990 2994 11248019 10.1073/pnas.061411798
23. Empirical parameters for calculating cation-oxygen bond valences. ID Brown KK Wu, Acta Crystallogr B 1976 B32 1957 1959 10.1107/S0567740876006869
24. Valence screening of water in protein crystals reveals potential Na+ binding sites. M Nayal E Di Cera, J Mol Biol 1996 256 2 228 234 10.1006/jmbi.1996.0081 8594192
25. The mechanism of ligand binding to the periplasmic C4-dicarboxylate binding protein (DctP) from Rhodobacter capsulatus. AR Walmsley JG Shaw DJ Kelly, J Biol Chem 1992 267 12 8064 8072 1569065
26. Glutamate transport in Rhodobacter sphaeroides is mediated by a novel binding protein-dependent secondary transport system. MH Jacobs T van der Heide AJ Driessen WN Konings, Proc Natl Acad Sci U S A 1996 93 23 12786 12790 8917497 10.1073/pnas.93.23.12786
27. Associative properties of the Escherichia coli galactose-binding protein and maltose-binding protein. G Richarme, Biochim Biophys Acta 1983 748 1 99 108 6351927
28. ABC transporters: one, two or four extracytoplasmic substrate-binding sites? T van der Heide B Poolman, EMBO Rep 2002 3 10 938 943 12370206 10.1093/embo-reports/kvf201
29. Structure of human lactoferrin at 3.2-A resolution. BF Anderson HM Baker EJ Dodson GE Norris SV Rumball JM Waters EN Baker, Proc Natl Acad Sci U S A 1987 84 7 1769 1773 3470756 10.1073/pnas.84.7.1769
30. ATP-binding cassette transporters in bacteria. AL Davidson J Chen, Annu Rev Biochem 2004 73 241 268 10.1146/annurev.biochem.73.011303.073626 15189142
31. Liganded and unliganded receptors interact with equal affinity with the membrane complex of periplasmic permeases, a subfamily of traffic ATPases. GF Ames CE Liu AK Joshi K Nikaido, J Biol Chem 1996 271 24 14264 14270 10.1074/jbc.271.24.14264 8662800
32. Trapping the transition state of an ATP-binding cassette transporter: evidence for a concerted mechanism of maltose transport. J Chen S Sharma FA Quiocho AL Davidson, Proc Natl Acad Sci U S A 2001 98 4 1525 1530 11171984 10.1073/pnas.041542498
33. Mechanism of coupling of transport to hydrolysis in bacterial ATP-binding cassette transporters. AL Davidson, J Bacteriol 2002 184 5 1225 1233 11844750
34. On the osmotic signal and osmosensing mechanism of an ABC transport system for glycine betaine. T van der Heide MC Stuart B Poolman, Embo J 2001 20 24 7022 7032 11742979 10.1093/emboj/20.24.7022
35. A papain-like enzyme at work: native and acyl-enzyme intermediate structures in phytochelatin synthesis. D Vivares P Arnoux D Pignol, Proc Natl Acad Sci U S A 2005 102 52 18848 18853 16339904 10.1073/pnas.0505833102
36. Autoindexing of rotation diffracton images and parameter refinement: 29-30 January 1993; SERC Daresbury Laboratory, Daresbury,UK. AGW Leslie,, Sawyer L, Isaacs N, Bailey S, 1993 44 51
37. The CCP4 suite: programs for protein crystallography. CCP4, Acta Crystallogr D Biol Crystallogr 1994 50 760-63
38. SOLVE and RESOLVE: automated structure solution and density modification. TC Terwilliger, Methods Enzymol 2003 374 22 37 14696367
39. Coot: model-building tools for molecular graphics. P Emsley K Cowtan, Acta Crystallogr D Biol Crystallogr 2004 60 Pt 12 Pt 1 2126 2132 10.1107/S0907444904019158 15572765
40. Refinement of macromolecular structures by the maximum-likelihood method. GN Murshudov AA Vagin EJ Dodson, Acta Crystallogr D Biol Crystallogr 1997 53 Pt 3 240 255 10.1107/S0907444996012255 15299926
41. PROCHECK: a program to check the stereochemical quality of protein structures. RA Laskowski MW MacArthur DS Moss JM Thornton, J Appl Crystallogr 1993 26 283 291 10.1107/S0021889892009944
42. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. M Landau I Mayrose Y Rosenberg F Glaser E Martz T Pupko N Ben-Tal, Nucleic Acids Res 2005 33 Web Server issue W299 302 15980475 10.1093/nar/gki370