Evolutionary relationship between 5+5 and 7+7 inverted repeat folds within the amino acid-polyamine-organocation superfamily

Proteins: Structure, Function and Bioinformatics

Volumn 82, Issue 2, 2014, Pages 336-346

  Västermark, Åke ^a   Saier, Milton H ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

AdiC; UraA; Amino acid polyamine organocation; APC; Duplication; Hairpin; Superfamily

Indexed keywords

AMINO ACID POLYAMINE ORGANOCATION PROTEIN; CARRIER PROTEIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; INVERTED REPEAT; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STRUCTURE;

ADIC; URAA; AMINO ACID-POLYAMINE-ORGANOCATION; APC; DUPLICATION; HAIRPIN; SUPERFAMILY;

AMINO ACID TRANSPORT SYSTEMS; ANIMALS; ANION TRANSPORT PROTEINS; EVOLUTION, MOLECULAR; HUMANS; INVERTED REPEAT SEQUENCES; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; RATS; REPETITIVE SEQUENCES, AMINO ACID; SEQUENCE ANALYSIS, PROTEIN; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 84892679519     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24401     Document Type: Article

References (39)

1. Forrest LR, Kramer R, Ziegler C. The structural basis of secondary active transport mechanisms. Biochim Biophys Acta 2011;1807:167-188.
2. Saier MH, Jr. Families of transmembrane transporters selective for amino acids and their derivatives. Microbiology 2000;146 (Part 8):1775-1795.
3. Forrest LR, Rudnick G. The rocking bundle: a mechanism for ion-coupled solute flux by symmetrical transporters. Physiology (Bethesda) 2009;24:377-386.
4. Wong FH, Chen JS, Reddy V, Day JL, Shlykov MA, Wakabayashi ST, Saier MH, Jr. The amino acid-polyamine-organocation superfamily. J Mol Microbiol Biotechnol 2012;22:105-113.
5. Reddy VS, Shlykov MA, Castillo R, Sun EI, Saier MH, Jr. The major facilitator superfamily (MFS) revisited. FEBS J 2012;279:2022-2035.
6. Jack DL, Paulsen IT, Saier MH. The amino acid/polyamine/organocation (APC) superfamily of transporters specific for amino acids, polyamines and organocations. Microbiology 2000;146 (Part 8):1797-1814.
7. Lu F, Li S, Jiang Y, Jiang J, Fan H, Lu G, Deng D, Dang S, Zhang X, Wang J, Yan N. Structure and mechanism of the uracil transporter UraA. Nature 2011;472:243-246.
8. Shaffer PL, Goehring A, Shankaranarayanan A, Gouaux E. Structure and mechanism of a Na+-independent amino acid transporter. Science 2009;325:1010-1014.
9. Singh SK, Yamashita A, Gouaux E. Antidepressant binding site in a bacterial homologue of neurotransmitter transporters. Nature 2007;448:952-956.
10. Weyand S, Shimamura T, Yajima S, Suzuki S, Mirza O, Krusong K, Carpenter EP, Rutherford NG, Hadden JM, O'Reilly J, Ma P, Saidijam M, Patching SG, Hope RJ, Norbertczak HT, Roach PC, Iwata S, Henderson PJ, Cameron AD. Structure and molecular mechanism of a nucleobase-cation-symport-1 family transporter. Science 2008;322:709-713.
11. Perez C, Koshy C, Yildiz O, Ziegler C. Alternating-access mechanism in conformationally asymmetric trimers of the betaine transporter BetP. Nature 2012;490:126-130.
12. Schulze S, Koster S, Geldmacher U, Terwisscha van Scheltinga AC, Kuhlbrandt W. Structural basis of Na(+)-independent and cooperative substrate/product antiport in CaiT. Nature 2010;467:233-236.
13. Watanabe A, Choe S, Chaptal V, Rosenberg JM, Wright EM, Grabe M, Abramson J. The mechanism of sodium and substrate release from the binding pocket of vSGLT. Nature 2010;468:988-991.
14. Gao X, Lu F, Zhou L, Dang S, Sun L, Li X, Wang J, Shi Y. Structure and mechanism of an amino acid antiporter. Science 2009;324:1565-1568.
15. Bernsel A, Viklund H, Hennerdal A, Elofsson A. TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res 2009;37(Web Server issue):W465-W468.
16. Krissinel E, Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 2004;60(Part 12, Part 1):2256-2268.
17. Khafizov K, Staritzbichler R, Stamm M, Forrest LR. A study of the evolution of inverted-topology repeats from LeuT-fold transporters using AlignMe. Biochemistry 2010;49:10702-10713.
18. Screpanti E, Hunte C. Discontinuous membrane helices in transport proteins and their correlation with function. J Struct Biol 2007;159:261-267.
19. Perez C, Ziegler C. Mechanistic aspects of sodium-binding sites in LeuT-like fold symporters. Biol Chem 2013;394:641-648.
20. Yamashita A, Singh SK, Kawate T, Jin Y, Gouaux E. Crystal structure of a bacterial homologue of Na+/Cl-dependent neurotransmitter transporters. Nature 2005;437:215-223.
21. Perez C, Khafizov K, Forrest LR, Kramer R, Ziegler C. The role of trimerization in the osmoregulated betaine transporter BetP. EMBO Rep 2011;12:804-810.
22. Tsai CJ, Khafizov K, Hakulinen J, Forrest LR, Kramer R, Kuhlbrandt W, Ziegler C. Structural asymmetry in a trimeric Na+/betaine symporter, BetP, from Corynebacterium glutamicum. J Mol Biol 2011;407:368-381.
23. Ressl S, Terwisscha van Scheltinga AC, Vonrhein C, Ott V, Ziegler C. Molecular basis of transport and regulation in the Na(+)/betaine symporter BetP. Nature 2009;458:47-52.
24. Schanzler M, Fahlke C. Anion transport by the cochlear motor protein prestin. J Physiol 2012;590 (Part 2):259-272.
25. Reddy VS, Saier MH, Jr. BioV Suite-a collection of programs for the study of transport protein evolution. FEBS J 2012;279:2036-2046.
26. Ebejer JP, Hill JR, Kelm S, Shi J, Deane CM. Memoir: template-based structure prediction for membrane proteins. Nucleic Acids Res 2013;41 (Web Server issue):W379-W383.
27. Neumann S, Hartmann H, Martin-Galiano AJ, Fuchs A, Frishman D. Camps 2.0: exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins. Proteins 2012;80:839-857.
28. Frillingos S. Insights to the evolution of nucleobase-ascorbate transporters (NAT/NCS2 family) from the Cys-scanning analysis of xanthine permease XanQ. Int J Biochem Mol Biol 2012;3:250-272.
29. Kosti V, Lambrinidis G, Myrianthopoulos V, Diallinas G, Mikros E. Identification of the substrate recognition and transport pathway in a eukaryotic member of the nucleobase-ascorbate transporter (NAT) family. PLoS One 2012;7:e41939.
30. Papakostas K, Frillingos S. Substrate selectivity of YgfU, a uric acid transporter from Escherichia coli. J Biol Chem 2012;287:15684-15695.
31. Karena E, Frillingos S. The role of transmembrane segment TM3 in the xanthine permease XanQ of Escherichia coli. J Biol Chem 2011;286:39595-39605.
32. Jack DL, Yang NM, Saier MH, Jr. The drug/metabolite transporter superfamily. Eur J Biochem 2001;268:3620-3639.
33. Li J, Shaikh SA, Enkavi G, Wen PC, Huang Z, Tajkhorshid E. Transient formation of water-conducting states in membrane transporters. Proc Natl Acad Sci USA 2013;110:7696-7701.
34. Jeschke G. A comparative study of structures and structural transitions of secondary transporters with the LeuT fold. Eur Biophys J 2013;42:181-197.
35. Schweikhard ES, Ziegler CM. Amino acid secondary transporters: toward a common transport mechanism. Curr Top Membr 2012;70:1-28.
36. Courville P, Urbankova E, Rensing C, Chaloupka R, Quick M, Cellier MF. Solute carrier 11 cation symport requires distinct residues in transmembrane helices 1 and 6. J Biol Chem 2008;283:9651-9658.
37. Grishin NV. Fold change in evolution of protein structures. J Struct Biol 2001;134:167-185.
38. Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005;21:951-960.
39. Spyropoulos IC, Liakopoulos TD, Bagos PG, Hamodrakas SJ. TMRPres2D: high quality visual representation of transmembrane protein models. Bioinformatics 2004;20:3258-3260.