The cis-Pro touch-turn: A rare motif preferred at functional sites

Proteins: Structure, Function and Genetics

Volumn 56, Issue 2, 2004, Pages 298-309

  Videau, Lizbeth L ^a   Arendall III, W Bryan ^a   Richardson, Jane S ^a  

^a DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

DNA polymerase; Glucoamylase; Ni Fe hydrogenase; Opine dehydrogenase; Pectate lyase; Phage gene 3 protein; Protein structure motif; Ribonuclease H; Ribotoxin; Structural bioinformatics; Xylanase

Indexed keywords

DNA DIRECTED DNA POLYMERASE BETA; GLUCAN 1,4 ALPHA GLUCOSIDASE; HYDROGENASE; IRON; NICKEL; OXIDOREDUCTASE; PECTATE LYASE; RIBONUCLEASE H; XYLAN ENDO 1,3 BETA XYLOSIDASE;

ARTICLE; BINDING SITE; BIOINFORMATICS; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE;

AMINO ACID MOTIFS; BINDING SITES; CATALYTIC DOMAIN; DATABASES, PROTEIN; ENZYMES; MODELS, MOLECULAR; PROTEIN BINDING; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 3042719944     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20101     Document Type: Article

References (58)

1. Venkatachalam CM. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 1968;6:1425-1436.
2. Richardson JS, Getzoff ED, Richardson DC. The beta bulge: a common small unit of non-repetitive protein structure. Proc Natl Acad Sci USA 1978;75:2574-2578.
3. Sibanda BL, Thornton JM. Beta-hairpin families in globular proteins. Nature 1985;316:170-174.
4. Sternberg MJE, Thornton JM. On the conformation of proteins: the handedness of the connection between parallel β-strands. J Mol Biol 1977;110:269-283.
5. Richardson JS. Handedness of crossover connections in beta sheets. Proc Natl Acad Sci USA 1976;73:2619-2623.
6. Kretsinger RH. Calcium-binding proteins. Annu Rev Biochem 1976;45:239-266.
7. Landschulz WH, Johnson PF, McKnight SL. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 1988;240:1759-1764.
8. Richardson JS, Richardson DC. Amino acid preferences for specific locations at the ends of α-helices. Science 1988;240:1648-1652.
9. Presta LG, Rose GD. Helix signals in proteins. Science 1988;240: 1632-1641.
10. Muñoz V, Blanco FJ, Serrano L. The hydrophobic-staple motif and a role for loop-residues in α-helix stability and protein folding. Nat Struct Biol 1995;2:380-385.
11. Richardson DC, Richardson JS. Principles and patterns of protein conformation. In: Fasman GD, editor. Prediction of protein structure and the principles of protein conformation. New York: Plenum; 1989. p 1-98.
12. Brandts JF, Halvorson HR, Brennan M. Consideration of the possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues. Biochemistry 1975;14:4953-4963.
13. Andreotti AH. Native state proline isomerization-an intrinsic molecular switch. Biochemistry 2003;42:9515-9524.
14. Lovell SC, Davis IW, Arendall WB III, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins 2003;50:437-450.
15. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
16. Lovell SC, Word JM, Richardson JS, Richardson DC. The penultimate rotamer library. Proteins 2000;40:389-408.
17. Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogens. J Mol Biol 1999;285:1711-1733.
18. Widenius M, Axmark D. MySQL Reference Manual. New York: O'Reilly & Associates, Inc.; 2002. pp. 712.
19. Richardson DC, Richardson JS. The kinemage: a tool for scientific illustration. Protein Sci 1992;1:3-9.
20. Richardson JS, Richardson DC. MAGE, PROBE, and kinemages. In: Rossmann MG, Arnold E, editors. International tables for crystallography. Volume F: crystallography of biological macromolecules. Dordrecht: Kluwer Academic; 2002. p 727-730.
21. Wu CH, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu Z-Z, Ledley RS, Lewis KC, Mewes H-W, Orcutt BC, Suzek BE, Tsugita A, Vinayaka CR, Yeh L-SL, Zhang J, Barker WC. The Protein Information Resource: an integrated public resource of functional annotation of proteins. Nucleic Acids Res 2002;30:35-37.
22. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25: 3389-3402.
23. Holm L, Sander C. DALI-A network tool for protein-structure comparison. Trends in Biochem Sci 1995;20:478-480.
24. Holm L, Sander C. Mapping the protein universe. Science 1996;273: 595-602.
25. Murzin A, Brenner SE, Hubband T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
26. Merritt EA, Bacon DJ. Raster3D: photorealistic molecular graphics. Methods Enzymol Macromol Crystallogr B 1997;277:505-524.
27. Karplus PA. Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Sci 1996;5:1406-1420.
28. Roach PL, Clifton IJ, Hensgens CM, Shibata N, Schofield CJ, Hajdu J, Baldwin JE. Structure of isopenicillin N synthase complexed with substrate and the mechanism of penicillin formation. Nature 1997;387:827-830.
29. Higuchi Y, Ogata H, Miki K, Yasuoka N, Yagi T. Removal of the bridging ligand atom at the Ni-Fe active site of [Nife] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 Å resolution. Structure 1999;7:549-556.
30. Herron SR, Benen JA, Scavetta RD, Visser J, Jurnak F. Structure and function of pectic enzymes: virulence factors of plant pathogens. Proc Natl Acad Sci USA 2000;97:8762-8769.
31. Vitali J, Schick B, Kester HCM, Visser J, Jurnak F. The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-Å resolution. Plant Physiol 1998;116:69-80.
32. Aleshin AE, Stoffer B, Firsov LM, Svensson B, Honzatko RB. Crystallographic complexes of glucoamylase with maltooligosaccharide analogs: relationship of stereochemical distortions at the nonreducing end to the catalytic mechanism. Biochemistry 1996; 35: 8319-8328.
33. Britton KL, Asano Y, Rice DW. Crystal structure and active site location of N-(1-D carboxylethyl)-L-norvaline dehydrogenase. Nature Struct Biol 1998;5:593-601.
34. Katayanagi K, Miyagawa M, Matsushima M, Ishikawa M, Kanaya S, Nakamura H, Ikehara M, Matsuzaki T, Morikawa K. Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution. J Mol Biol 1992;223:1029-1052.
35. Kiefer JR, Mao C, Hansen CJ, Basehore SL, Hogrefe HH, Braman JC, Beese LS. Crystal structure of a thermostable bacillus DNA polymerase I large fragment at 2.1 Å resolution. Structure 1997;5: 95-108.
36. Yang X, Moffat K. Insights into specificity of cleavage and mechanism of cell entry from the crystal structure of the highly specific aspergillus ribotoxin, restrictocin. Structure 1996;4: 837.
37. Yang X, Gerczei T, Glover LT, Correll CC. Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping. Nature Struct Biol 2001;8:968-973.
38. Leontis NB, Westhof E. A common motif organizes the structure of multi-helix loops in 16S and 23S ribosomal RNAs. J Mol Biol 1998;283:571-583.
39. Lubkowski J, Henneeke F, Pltickthun A, Wlodawer A. The structural basis of phage display elucidated by the crystal structure of the N-terminal domains of g3p. Nature Struct Biol 1998;5:140-147.
40. Deng L-W, Malik P, Perham RN. Interaction of the globular domains of pIII protein of filamentous bacteriophage fd with the F-pilus of Escherichia coli. Virology 1999;253:271-277.
41. Conti E, Kuriyan J. Crystallographic analysis of the specific yet versatile recognition of distinct nuclear localization signals by karyopherin alpha. Structure 2000;8:329-338.
42. Sakon J, Irwin D, Wilson DB, Karplus PA. Structure and mechanism of endo/exocellulase E4 from Thermomonospora fusca. Nature Struct Biol 1997;4:810-818.
43. Sugantino M, Roderick SL. Crystal structure of Vat(D): an acetyl-transferase that inactivates streptogramin group A antibiotics. Biochemistry 2002;41:2209-2216.
44. Beaman TW, Blanchard JS, Roderick SL. The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase. Biochemistry 1998;37:10363-10369.
45. Karplus PA, Schulz GE. Refined structure of glutathione reductase at 1.54 Å resolution. J Mol Biol 1987;195:701-729.
46. a. Kim Y, Geiger JH, Hahn S, Sigler PB. Crystal structure of a yeast TBP/TATA-box complex. Nature 1993;365:512-520.
47. b. Merritt EA, Kuhn P, Sarfaty S, Erbe JL, Holmes RK, Hol WJG. The 1.25 Å resolution refinement of the cholera toxin B-pentamer: evidence of peptide backbone strain at the receptor-binding site. J Mol Biol 1998;282:1043-1059.
48. Guss JM, Bartunik HD, Freeman HC. Accuracy and precision in protein structure analysis: restrained least-squares refinement of the structure of poplar plastocyanin at 1.33 Å resolution. Acta Crystallogr B 1992;48:790-811.
49. Williams PA, Blackburn NJ, Sanders D, Bellamy H, Stura EA, Fee JA, McRee DE. The CuA domain of Thermus thermophilus ba3-type cytochrome c oxidase at 1.6 Å resolution. Nature Struct Biol 1999;6:509-516.
50. Bullock TL, Roberts TM, Stewart M. 2.5 Å resolution crystal structure of the motile major sperm protein (MSP) of Ascaris suum. J Mol Biol 1996;263:284-296.
51. Richardson JS, Richardson DC. Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc Natl Acad Sci USA 2002;99:2754-2759.
52. Wlodawer A, Svensson LA, Sjölin L, Gilliland GL. Structure of phosphate-free ribonuclease A refined at 1.26 Å. Biochemistry 1988;27:2705-2717.
53. Li Y, Mitaxov V, Waksman G. Structure-based design of novel Taq DNA polymerase with improved properties of dideoxynucleotide incorporation. Proc Natl Acad Sci USA 1999;96:9491.
54. Engh RA, Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr A 1991;47:392-400.
55. Kiefer JR, Mao C, Braman JC, Beese LS. Visualizing DNA replication in a catalytically active bacillus DNA polymerase crystal. Nature 1998;391:304-307.
56. Gunasekaran K, Gomathi L, Ramakrishnan C, Chandrasekhar J, Balaram P. Conformational interconversions in peptide β-turns: analysis of turns in proteins and computational estimates of barriers. J Mol Biol 1998;284:1505-1516.
57. Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 1999b;285:1735-1747.
58. Beaman TW, Sugantino M, Roderick SL. Structure of the hexapeptide xenobiotic acetyltransferase from Pseudomonas aeruginosa. Biochemistry 1998;37:6689-6696.