Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 28, 2013, Pages 11343-11348

  Doki, Shintaro ^a,b   Hideaki E Kato, ^a,b   Solcan, Nicolae ^c   Iwaki, Masayo ^d   Koyama, Michio ^a   Hattori, Motoyuki ^a,e   Iwase, Norihiko ^f   Tsukazaki, Tomoya ^a,b,e   Sugita, Yuji ^b   Kandori, Hideki ^d   Newstead, Simon ^c   Ishitani, Ryuichiro ^a,b   Osamu Nureki, ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b RIKEN   (Japan)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d NAGOYA INSTITUTE OF TECHNOLOGY   (Japan)

^e JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^f TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Membrane transporter; Molecular dynamics simulation; X ray crystallography

Indexed keywords

ALAFOSFALIN; GLUTAMIC ACID; PEPTIDE TRANSPORTER 1; PROTON DEPENDENT OLIGOPEPTIDE TRANSPORTER; SODIUM CHLORIDE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENDOSPORE-FORMING RODS AND COCCI; GEOBACILLUS KAUSTOPHILUS; HYDROGEN BOND; INTRACELLULAR SPACE; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; PROTEIN TRANSPORT;

MEMBRANE TRANSPORTER; MOLECULAR DYNAMICS SIMULATION; X-RAY CRYSTALLOGRAPHY;

ALANINE; CARRIER PROTEINS; ION TRANSPORT; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PROTEIN CONFORMATION; PROTONS;

BACTERIA (MICROORGANISMS);

EID: 84879895875     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1301079110     Document Type: Article

References (38)

1. Yan N (2013) Structural advances for the major facilitator superfamily (MFS) transporters. Trends Biochem Sci 38(3):151-159.
2. Reddy VS, Shlykov MA, Castillo R, Sun EI, Saier MH, Jr. (2012) The major facilitator superfamily (MFS) revisited. FEBS J 279(11):2022-2035.
3. Guan L, Kaback HR (2006) Lessons from lactose permease. Annual Review of Biophysics and Biomolecular Structure, Annual Review of Biophysics ( Annual Reviews, Palo Alto), Vol 35, pp 67-91.
4. Smirnova I, Kasho V, Sugihara J, Kaback HR (2009) Probing of the rates of alternating access in LacY with Trp fluorescence. Proc Natl Acad Sci USA 106(51):21561-21566.
5. Radestock S, Forrest LR (2011) The alternating-access mechanism of MFS transporters arises from inverted-topology repeats. J Mol Biol 407(5):698-715.
6. Abramson J, et al. (2003) Structure and mechanism of the lactose permease of Escherichia coli. Science 301(5633):610-615. (Pubitemid 36927939)
7. Mirza O, Guan L, Verner G, Iwata S, Kaback HR (2006) Structural evidence for induced fit and a mechanism for sugar/H+ symport in LacY. EMBO J 25(6):1177-1183.
8. Guan L, Mirza O, Verner G, Iwata S, Kaback HR (2007) Structural determination of wild-type lactose permease. Proc Natl Acad Sci USA 104(39):15294-15298. (Pubitemid 47502911)
9. Huang YF, Lemieux MJ, Song JM, Auer M, Wang DN (2003) Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli. Science 301(5633):616-620. (Pubitemid 36927940)
10. Pedersen BP, et al. (2013) Crystal structure of a eukaryotic phosphate transporter. Nature 496(7446):533-536.
11. Yin Y, He X, Szewczyk P, Nguyen T, Chang G (2006) Structure of the multidrug transporter EmrD from Escherichia coli. Science 312(5774):741-744.
12. Yan H, et al. (2013) Structure and mechanism of a nitrate transporter. Cell Rep 3(3):716-723.
13. Sun LF, et al. (2012) Crystal structure of a bacterial homologue of glucose transporters GLUT1-4. Nature 490(7420):361-366.
14. Dang SY, et al. (2010) Structure of a fucose transporter in an outward-open conformation. Nature 467(7316):734-738.
15. Forrest LR, Kramer R, Ziegler C (2011) The structural basis of secondary active transport mechanisms. Biochim. Biophys. Acta-Bioenerg. 1807(2):167-188.
16. Paulsen IT, Skurray RA (1994) The POT family of transport proteins. Trends Biochem Sci 19(10):404. (Pubitemid 24320128)
17. Steiner HY, Naider F, Becker JM (1995) The PTR family: a new group of peptide transporters. Mol Microbiol 16(5):825-834.
18. Ganapathy V, Leibach FH (1983) Role of pH gradient and membrane potential in dipeptide transport in intestinal and renal brush-border membrane vesicles from the rabbit. Studies with L-carnosine and glycyl-L-proline. J Biol Chem 258(23):14189-14192. (Pubitemid 14217939)
19. Daniel H, Spanier B, Kottra G, Weitz D (2006) From bacteria to man: archaic protondependent peptide transporters at work. Physiology (Bethesda) 21:93-102. (Pubitemid 43752505)
20. Fei YJ, et al. (1994) Expression cloning of a mammalian proton-coupled oligopeptide transporter. Nature 368(6471):563-566.
21. Covitz KMY, Amidon GL, Sadée W (1998) Membrane topology of the human dipeptide transporter, hPEPT1, determined by epitope insertions. Biochemistry 37(43):15214-15221. (Pubitemid 28503250)
22. Smith DE, Clémençon B, Hediger MA (2013) Proton-coupled oligopeptide transporter family SLC15: physiological, pharmacological and pathological implications. Mol Aspects Med 34(2-3):323-336.
23. Wenzel U, Thwaites DT, Daniel H (1995) Stereoselective uptake of beta-lactam antibiotics by the intestinal peptide transporter. Br J Pharmacol 116(7):3021-3027.
24. Tamai I, et al. (1997) The predominant contribution of oligopeptide transporter PepT1 to intestinal absorption of beta-lactam antibiotics in the rat small intestine. J Pharm Pharmacol 49(8):796-801. (Pubitemid 27386903)
25. Faria TN, et al. (2004) A novel high-throughput pepT1 transporter assay differentiates between substrates and antagonists. Mol Pharm 1(1):67-76.
26. Ganapathy ME, Huang W, Wang H, Ganapathy V, Leibach FH (1998) Valacyclovir: a substrate for the intestinal and renal peptide transporters PEPT1 and PEPT2. Biochem Biophys Res Commun 246(2):470-475. (Pubitemid 28412626)
27. Newstead S, et al. (2011) Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2. EMBO J 30(2):417-426.
28. Solcan N, et al. (2012) Alternating access mechanism in the POT family of oligopeptide transporters. EMBO J 31(16):3411-3421.
29. Harder D, et al. (2008) DtpB (YhiP) and DtpA (TppB, YdgR) are prototypical protondependent peptide transporters of Escherichia coli. FEBS J 275(13):3290-3298. (Pubitemid 351813542)
30. Weitz D, et al. (2007) Functional and structural characterization of a prokaryotic peptide transporter with features similar to mammalian PEPT1. J Biol Chem 282(5):2832-2839. (Pubitemid 47084338)
31. Neumann J, Bruch M, Gebauer S, Brandsch M (2004) Transport of the phosphonodipeptide alafosfalin by the H+/peptide cotransporters PEPT1 and PEPT2 in intestinal and renal epithelial cells. Eur J Biochem 271(10):2012-2017. (Pubitemid 38657353)
32. Xu LY, Haworth IS, Kulkarni AA, Bolger MB, Davies DL (2009) Mutagenesis and cysteine scanning of transmembrane domain 10 of the human dipeptide transporter. Pharm Res 26(10):2358-2366.
33. Fang G, Konings WN, Poolman B (2000) Kinetics and substrate specificity of mem-brane- reconstituted peptide transporter DtpT of Lactococcus lactis. J Bacteriol 182(9):2530-2535. (Pubitemid 30212912)
34. Yin Y, Jensen MO, Tajkhorshid E, Schulten K (2006) Sugar binding and protein conformational changes in lactose permease. Biophys J 91(11):3972-3985. (Pubitemid 44889188)
35. Holyoake J, Sansom MSP (2007) Conformational change in an MFS protein: MD simulations of LacY. Structure 15(7):873-884. (Pubitemid 47042433)
36. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50(Pt 5):760-763.
37. Adams PD, et al. (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58(Pt 11):1948-1954. (Pubitemid 35337293)
38. Phillips JC, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26(16):1781-1802. (Pubitemid 43078511)