Solution structure and binding specificity of FBP11/HYPA WW domain as group-II/III

Proteins: Structure, Function and Genetics

Volumn 63, Issue 1, 2006, Pages 227-234

  Kato, Yusuke ^a   Hino, Yumi ^a   Nagata, Koji ^a   Tanokura, Masaru ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; FORMIN BINDING PROTEIN 11; HUNTINGTIN YEAST PARTNER A PROTEIN; HYDROGEN; NITROGEN 15; PROLINE; UNCLASSIFIED DRUG;

ARTICLE; EUKARYOTE; HYDROPHOBICITY; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; PROTON NUCLEAR MAGNETIC RESONANCE; TITRIMETRY;

AMINO ACID SEQUENCE; ANIMALS; HUMANS; HYDROGEN; HYDROGEN BONDING; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTEOMICS; SEQUENCE HOMOLOGY, AMINO ACID; SURFACE PLASMON RESONANCE;

EUKARYOTA;

EID: 33645022000     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20880     Document Type: Article

References (32)

1. Lin KT, Lu RM, Tarn WY. The WW domain-containing proteins interact with the early spliceosome and participate in pre-mRNA splicing in vivo. Mol Cell Biol 2004;24:9176-9185.
2. Faber PW, Barnes GT, Srinidhi J, Chen J, Gusella JF, MacDonald ME. Huntingtin interacts with a family of WW domain proteins. Hum Mol Genet 1998;7:1463-1474.
3. Chan DC, Bedford MT, Leder P. Formin binding proteins bear WWP/WW domains that bind proline-rich peptides and functionally resemble SH3 domains. EMBO J 1996;15:1045-1054.
4. Kato Y, Nagata K, Takahashi M, Lian L, Herrero JJ, Sudol M, Tanokura M. Common mechanism of ligand recognition by group II/III WW domains: redefining their functional classification. J Biol Chem 2004;279:31833-31841.
5. Simpson GG, Dijkwel PP, Quesada V, Henderson I, Dean C. FY is an RNA 3′ end-processing factor that interacts with FCA to control the Arabidopsis floral transition. Cell 2003;113:777-787.
6. Zarrinpar A, Lim WA. Converging on proline: the mechanism of WW domain peptide recognition. Nat Struct Biol 2000;7:611-613.
7. Huang X, Poy F, Zhang R, Joachimiak A, Sudol M, Eck MJ. Structure of a WW domain containing fragment of dystrophin in complex with beta-dystroglycan. Nat Struct Biol 2000;7:634-638.
8. Sudol M, Hunter T. NeW wrinkles for an old domain. Cell 2000;103:1001-1004.
9. Kato Y, Ito M, Kawai K, Nagata K, Tanokura, M. Determinants of ligand specificity in groups I and IV WW domains as studied by surface plasmon resonance and model building. J Biol Chem 2002;277:10173-10177.
10. Otte L, Wiedemann U, Schlegel B, Pires JR, Beyermann M, Schmieder P, Krause G, Volkmer-Engert R, Schneider-Mergener J, Oschkinat H. WW domain sequence activity relationships identified using ligand recognition propensities of 42 WW domains. Protein Sci 2003;12:491-500.
11. Espanel X, Navin N, Kato Y, Tanokura M, Sudol M. Probing WW domains to uncover and refine determinants of specificity in ligand recognition. Cytotechnology 2003;43:105-111.
12. Hu H, Columbus J, Zhang Y, Wu D, Lian L, Yang S, Goodwin J, Luczak C, Carter M, Chen L, James M, Davis R, Sudol M, Rodwell J, Herrero JJ. A map of WW domain family interactions. Proteomics 2004;4:643-655.
13. Macias MJ, Wiesner S, Sudol M. WW and SH3 domains, two different scaffolds to recognize proline-rich ligands. FEBS Lett 2002;513:30-37.
14. Komuro A, Saeki M, Kato S. Association of two nuclear proteins, Npw38 and NpwBP, via the interaction between the WW domain and a novel proline-rich motif containing glycine and arginine. J Biol Chem 1999;274:36513-36519.
15. Pires JR, Parthier C, Aido-Machado R, Wiedemann U, Otte L, Bohm G, Rudolph R, Oschkinat H. Structural basis for APPTPP-PLPP peptide recognition by the FBP11WW1 domain. J Mol Biol 2005;348:399-408.
16. Kato Y, Sawano Y, Tanokura M. Expression and purification of active WW domains of FBP11/HYPA and FBP28/CA150. Protein Peptide Lett. Forthcoming.
17. 13C-and refocusing edited pulse schemes using broadband shaped inversion and refocusing pulses. J Magn Reson B 1996;112:63-68.
18. Cavanagh J, Fairbrother WJ, Palmer III AG, Skelton NJ. Protein NMR spectroscopy: principles and practice. New York: Academic Press; 1996.
19. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 1995;6:277-293.
20. Goddard TD, Kneller DG. SPARKY3. San Francisco: University of California.
21. 13C of protein chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 1994;4:171-180.
22. Guntert P, Mumenthaler C, Wüthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 1997;273:283-298.
23. Herrmann T, Güntert P, Wüthrich K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 2002;319:209-227.
24. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PRO-CHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993;26:283-291.
25. Macias MJ, Gervais V, Civera C, Oschkinat H. Structural analysis of WW domains and design of a WW prototype. Nat Struct Biol 2000;7:375-379.
26. Wiesner S, Stier G, Sattler M, Macias MJ. Solution structure and ligand recognition of the WW domain pair of the yeast splicing factor Prp40. J Mol Biol 2002;324:807-822.
27. Bedford MT, Reed R, Leder P. WW domain-mediated interactions reveal a spliceosome-associated protein that binds a third class of proline-rich motif: the proline glycine and methionine-rich motif. Proc Natl Acad Sci U S A 1998;95:10602-10607.
28. Espanel X, Sudol M. A single point mutation in a group I WW domain shifts its specificity to that of group II WW domains. J Biol Chem 1999;274:17284-17289.
29. Holbert S, Denghien I, Kiechle T, Rosenblatt A, Wellington C, Hayden MR, Margolis RL, Ross CA, Dausset J, Ferrante RJ, Neri C. The Gin-Ala repeat transcriptional activator CA150 interacts with huntingtin: neuropathologic and genetic evidence for a role in Huntington's disease pathogenesis. Proc Natl Acad Sci U S A 2001;98:1811-1816.
30. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O'Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Lewis S. Comparative genomics of the eukaryotes. Science 2000;287:2204-2215.
31. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997;18:2714-2723.
32. Koradi R, Billeter M, Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996;14:51-55.