Structural Principles of Leucine-Rich Repeat (LRR) Proteins

Proteins: Structure, Function and Genetics

Volumn 54, Issue 3, 2004, Pages 394-403

  Enkhbayar, Purevjav ^a,b   Kamiya, Masakatsu ^a,b   Osaki, Mitsuru ^a   Matsumoto, Takeshi ^b   Matsushima, Norio ^b  

^a HOKKAIDO UNIVERSITY   (Japan)

^b SAPPORO MEDICAL UNIVERSITY   (Japan)

Author keywords

sheet direction vector; Curvature; Geometric analysis; M bius strip; Three dimensional circle fitting; Tilt angle; Twist

Indexed keywords

LEUCINE; LEUCINE RICH REPEAT PROTEIN; PROTEIN; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BETA SHEET; BETA SHEET DIRECTION VECTOR; CHEMICAL STRUCTURE; CHEMISTRY; CONSENSUS SEQUENCE; CURVATURE; GEOMETRY; HUMAN; LEUCINE RICH REPEAT; MOBIUS STRIP; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; QUANTITATIVE ANALYSIS; STRUCTURE ANALYSIS; THREE DIMENSIONAL CIRCLE FITTING; TILT ANGLE; TWIST;

AMINO ACID MOTIFS; ANIMALS; CONSENSUS SEQUENCE; HUMANS; LEUCINE; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; REPETITIVE SEQUENCES, AMINO ACID;

EUKARYOTA;

EID: 1042291215     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10605     Document Type: Article

References (40)

1. Kobe B, Deisenhofer J. The leucine-rich repeat: a versatile binding motif. Trends Biochem Sci 1994;19:415-421.
2. Kobe B, Deisenhofer J. Proteins with leucine-rich repeats. Curr Opin Struct Biol 1995;5:409-416.
3. Kajava AV. Structural diversity of leucine-rich repeat proteins. J Mol Biol 1998;277:519-527.
4. Ohyanagi T, Matsushima N. Classification of tandem leucine-rich repeats within a great variety of proteins. FASEB J 1997;11:A949.
5. Kajava AV, Vassart G, Wodak SJ. Modeling of the three-dimensional structure of proteins with the typical leucine-rich repeats. Structure 1995;3:867-877.
6. Matsushima N, Ohyanagi T, Tanaka T, Kretsinger RH. Supermotifs and evolution of tandem leucine-rich repeats within the small proteoglycans-biglycan, decorin, lumican, fibromodulin, PRELP, keratocan, osteoadherin, epiphycan, and osteoglycin. Proteins 2000;38:210-225.
7. Kajava AV. Review: proteins with repeated sequence-structural prediction and modeling. J Struct Biol 2001;134:132-144.
8. Kobe B, Deisenhofer J. Crystal structure of porcine ribonuclease inhibitor, a protein with leucine-rich repeats. Nature 1993;366:751-756.
9. Papageorgiou AC, Shapiro R, Acharya KR. Molecular recognition of human angiogenin by placental ribonuclease inhibitor-an X-ray crystallographic study at 2.0 A resolution. EMBO J 1997;16: 5162-5177.
10. Hillig RC, Renault L, Vetter IR, Drell T IV, Wittinghofer A, Becker J. The crystal structure of RNA1p: a new fold for a GTPase-activating protein. Mol Cell 1999;3:781-791.
11. Seewald MJ, Korner C, Wittinghofer A, Vetter IR. RanGAP mediates GTP hydrolysis without an arginine finger. Nature 2002;415:662-666.
12. Schulman BA, Carrano AC, Jeffrey PD, Bowen Z, Kinnucan ER, Finnin MS, Elledge SJ, Harper JW, Pagano M, Pavletich NP. Insights into SCF ubiquitin ligases from the structure of the Skp1-Skp2 complex. Nature 2000;408:381-386.
13. Zheng N, Schulman BA, Song L, Miller JJ, Jeffrey PD, Wang P, Chu C, Koepp DM, Elledge SJ, Pagano M, Conaway RC, Conaway JW, Harper JW, Pavletich NP. Structure of the Cull-Rbx1-Skp1-F box Skp2 SCF ubiquitin ligase complex. Nature 2002;416:703-709.
14. Marino M, Braun L, Cossart P, Ghosh P. Structure of the lnlB leucine-rich repeats, a domain that triggers host cell invasion by the bacterial pathogen L. monocytogenes. Mol Cell 1999;4:1063-1072.
15. Schubert WD, Gobel G, Diepholz M, Darji A, Kloer D, Hain T, Chakraborty T, Wehland J, Domann E, Heinz DW. Internalins from the human pathogen Listeria monocytogenes combine three distinct folds into a contiguous internalin domain. J Mol Biol 2001;312:783-794.
16. Schubert WD, Urbanke C, Ziehm T, Beier V, Machner MP, Domann E, Wehland J, Chakraborty T, Heinz DW. Structure of internalin, a major invasion protein of Listeria monocytogenes, in complex with its human receptor E-cadherin. Cell 2002;111:825-836.
17. Zhang H, Seabra MC, Deisenhofer J. Crystal structure of Rab geranylgeranyltransferase at 2.0 Å resolution. Structure 2000;8: 241-251.
18. Liker E, Fernandez E, Izaurralde E, Conti E. The structure of the mRNA export factor TAP reveals a cis arrangement of a noncanonical RNP domain and an LRR domain. EMBO J 2000;19: 5587-5598.
19. Ho DN, Coburn GA, Kang Y, Cullen BR, Georgiadis MM. The crystal structure and mutational analysis of a novel RNA-binding domain found in the human Tap nuclear mRNA export factor. Proc Natl Acad Sci USA 2002;99:1888-1893.
20. Price SR, Evans PP, Nagai K. Crystal structure of the spliceosomal U2B-U2A protein complex bound to a fragment of U2 small nuclear RNA. Nature 1998;394:645-650.
21. Evdokimov AG, Anderson DE, Routzahn KM, Waugh DS. Unusual molecular arcitecture of the Yersinia pestis cytotoxin YopM: a leucine-rich repeat protein with the shortest repeating unit. J Mol Biol 2001;312:807-821.
22. Wu H, Maciejewski MW, Marintchev A, Benashski SE, Mullen GP, King SM. Solution structure of a dynein motor domain associated light chain. Nat Struct Biol 2000;7:575-579.
23. Wu H, Blackledge M, Maciejewski MW, Mullen GP, King SM. Relaxation-based structure refinement and backbone molecular dynamics of the dynein motor domain-associated light chain. Biochemistry 2003;42:57-71.
24. Uff S, Clemetson JM, Harrison T, Clemetson KJ, Emsley J. Crystal structure of the platelet glycoprotein Ibalpha N-terminal domain reveals an unmasking mechanism for receptor activation. J Biol Chem 2002;277:35657-35663.
25. Huizinga EG, Tsuji S, Romijn RA, Schiphorst ME, de Groot PG, Sixma JJ, Gros P. Structures of glycoprotein Ibα and its complex with von Willebrand factor A1 domain. Science 2002;297:1176-1179.
26. Krieger I, Kostyukova A, Yamashita A, Nitanai Y, Maeda Y. Crystal structure of the C-terminal half of tropomodulin and structural basis of actin filament pointed-end capping. Biophys J 2002;83:2716-2725.
27. He XL, Bazan JF, McDermott G, Park JB, Wang K, Tessier-Lavigne M, He Z, Garcia KC. Structure of the nogo receptor ectodomain: a recognition module implicated in myelin inhibition. Neuron 2003;38:177-185.
28. Kobe B, Kajava AV. When protein folding is simplified to protein coiling: the continuum of solenoid protein structures. Trends Biochem Sci 2000;25:509-515.
29. Shakarji CM. Least-squares fitting algorithms of the NIST algorithm testing system. J Res Natl Inst Stand 1998;103:633-641.
30. Kobe B, Kajava AV. The leucine-rich repeat as a protein recognition motif. Curr Opin Struct Biol 2001;11:725-732.
31. Kajava AV, Kobe B. Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information. Protein Sci 2002;1:1082-1090.
32. Murzin AG, Lesk AM, Chothia C. Principles determining the structure of beta-sheet barrels in proteins: I. A theoretical analysis. J Mol Biol 1994;236:1369-1381.
33. Murzin AG, Lesk AM, Chothia C. Principles determining the structure of beta-sheet barrels in proteins: II. The observed structures. J Mol Biol 1994;236:1382-1400.
34. Lasters I, Wodak SJ, Alard P, van Cutsem E. Structural principles of parallel beta-barrels in proteins. Proc Natl Acad Sci USA 1988;85:3338-3342.
35. Janin J, Chothia C. Packing of alpha-helices onto beta-pleated sheets and the anatomy of alpha/beta proteins. J Mol Biol 1980;143:95-128.
36. Chothia C, Janin J. Relative orientation of close packed β-sheets in proteins. Proc Natl Acad Sci USA 1981;74:4130-4134.
37. Novotny J, Bruccoleri RE, Newell J. Twisted hyperboloid (Strophoid) as a model of β-barrels in proteins. J Mol Biol 1984;177:567-573.
38. Kobe B, Deisenhofer J. A structural basis of the interactions between leucine-rich repeats and protein ligands. Nature 1995;374: 183-186.
39. Kobe B, Deisenhofer J. Complex between bovine ribonuclease A and porcine ribonuclease inhibitor crystallizes in a similar unit cell as free ribonuclease inhibitor. J Mol Biol 1994;241:288-291.
40. Forrer P, Stumpp MT, Binz HK, Pluckthun A. A novel strategy to design binding molecules harnessing the modular nature of repeat proteins. FEBS Lett 2003;539:2-6.