Crystal structures and properties of de novo circularly permuted 1,3- 1,4-β-glucanases

Proteins: Structure, Function and Genetics

Volumn 30, Issue 2, 1998, Pages 155-167

  Aÿ, Jacqueline ^a   Hahn, Michael ^a,d   Decanniere, Klaas ^a   Piotukh, Kirill ^b   Borriss, Rainer ^b   Heinemann, Udo ^a,c,e  

^a MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^b HUMBOLDT UNIVERSITY   (Germany)

^c FREIE UNIVERSITÄT BERLIN   (Germany)

^d NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^e NONE   (Germany)

Author keywords

1,3 1,4 glucanase; Circular permutation; Genetic engineering; Protein folding; X ray diffraction

Indexed keywords

1,3 BETA GLUCANASE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVITY; HYDROLYSIS; MOLECULAR EVOLUTION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE;

AMINO ACID SEQUENCE; BACILLUS; BACTERIAL PROTEINS; BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; ENZYME STABILITY; GLYCOSIDE HYDROLASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, DNA;

BACILLUS LICHENIFORMIS; ESCHERICHIA COLI; FIBROBACTER SUCCINOGENES; PAENIBACILLUS MACERANS;

EID: 0032005329     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980201)30:2<155::AID-PROT5>3.0.CO;2-M     Document Type: Article

References (50)

1. Creighton, T.E. Proteins: Structures and Molecular Properties, 2nd ed. New York: Freeman, 1993.
2. Pace, C.N., Heinemann, U., Hahn, U., Saenger, W. Ribonuclease T1: Structure, function, and stability. Angew. Chem. Int. Ed. Engl. 30:343-360, 1991.
3. Matthews, B.W. Studies on protein stability with T4 lysozyme. Adv. Protein Chem. 46:249-278, 1996.
4. Hahn, M., Olsen, O., Politz, O., Borriss, R., Heinemann, U. Crystal structure and site-directed mutagenesis of Bacillus macerans endo-1,3-1,4-β-glucanase. J. Biol. Chem. 270: 3081-3088, 1995.
5. Hahn, M., Pons, J., Planas, A., Querol, E., Heinemann, U. Crystal structure of Bacillus licheniformis 1,3-1,4-β-D-glucan 4-glucanohydrolase at 1.8 Å resolution. FEBS Letters 374:221-224, 1995.
6. Olsen, O., Borriss, R., Simon, O., Thomsen, K.K. Hybrid Bacillus (1-3,1-4)-β-glucanases: Engineering thermostable enzymes by construction of hybrid genes. Mol. Gen. Genet. 225:177-185, 1991.
7. Politz, O., Simon, O., Olsen, O., Borriss, R. Determinants for the enhanced thermostability of hybrid (1,3-1,4)-β-glucanases. Eur. J. Biochem. 216:829-834, 1993.
8. Keitel, T., Simon, O., Borriss, R., Heinemann, U. Molecular and active-site structure of a Bacillus 1,3-1,4-β-glucanase. Proc. Natl. Acad. Sci. USA 90:5287-5291, 1993.
9. Hahn, M., Keitel, T., Heinemann, U. Crystal and molecular structure at 0.16 nm resolution of the hybrid Bacillus endo-1,3-1,4-β-D-glucan 4-glucanohydrolase H(A16-M). Eur. J. Biochem. 232:849-858, 1995.
10. Keitel, T., Meldgaard, M., Heinemann, U. Cation binding to a Bacillus (1,3-1,4)-β-glucanase. Geometry, affinity and effect on protein stability. Eur. J. Biochem. 222:203-214, 1994.
11. Heinemann, U., Aÿ, J., Gaiser, O., Müller, J.J., Ponnuswamy, M.N. Enzymology and folding of natural and engineered bacterial β-glucanases studied by X-ray crystallography. Biol. Chem. 377:447-454, 1996.
12. Hahn, M., Piotukh, K., Borriss, R., Heinemann, U. Native-like in vivo folding of a circularly permuted jellyroll protein shown by crystal structure analysis. Proc. Natl. Acad. Sci. USA 91:10417-10421, 1994.
13. Teather, R.M., Erfle, J.D. DNA sequence of a Fibrobacter succinogenes mixed-linkage glucanase (1,3-1,4-β-D-glucan 4-glucanohydrolase) gene. J. Bacteriol. 172:3837-3841, 1990.
14. Schimming, S., Schwarz, W.H., Staudenbauer, W.L. Structure of the Clostridium thermocellum gene licB and the encoded β-1,3-1,4-glucanase. Eur. J. Biochem. 204:13-19, 1992.
15. Delarue, M., Poterszman, A., Nikonov, S., Garber, M., Moras, D., Thierry, J.C. Crystal structure of a prokaryotic aspartyl tRNA synthetase. EMBO J. 13:3219-3229, 1994.
16. Ponting, C.P., Russell, R.B. Swaposins: Circular permutations within genes encoding saposin homologues. Trends Biochem. Sci. 20:179-180, 1995.
17. Heinemann, U., Hahn, M. Circular permutations of protein sequence: Not so rare? Trends Biochem. Sci. 20:349-350, 1995.
18. Lupas, A. A circular permutation event in the evolution of the SLH domain? Mol. Microbiol. 20:897-898, 1996.
19. Lindqvist, Y., Schneider, G. Circular permutations of natural protein sequences: Structural evidence. Current Opinion Struct. Biol. 7:422-427, 1997.
20. Luger, K., Hommel, U., Herold, M., Hofsteenge, J., Kirschner, K. Correct folding of circularly permuted variants of a βα barrel enzyme in vivo. Science 243:206-210, 1989.
21. Heinemann, U., Hahn, M. Circular permutation of polypeptide chains: Implications for protein folding and stability. Prog. Biophys. Mol. Biol. 64:121-143, 1996.
22. Vignais, M.-L., Corbier, C., Mulliert, G., Branlant, C., Branlant, G. Circular permutation within the coenzyme binding domain of the tetrameric glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus. Protein Sci. 4:994-1000, 1995.
23. Koebnik, R., Krämer, L. Membrane assembly of circularly permuted variants of the E. coli outer membrane protein OmpA. J. Mol. Biol. 250:617-626, 1995.
24. Viguera, A.R., Serrano, L., Willmanns, M. Different folding transitions may result in the same native structure. Nature Struct. Biol. 3:874-880, 1996.
25. Horton, R.M., Hunt, H.D., Ho, S.N., Pullen, J.K., Pease, L.R. Engineering hybrid genes without the use of restriction enzymes: Gene splicing by overlap extension. Gene 77: 61-68, 1989.
26. Jancarik, J., Kim, S.-H. Sparse matrix sampling: A screening method for crystallization of proteins. J. Appl. Crystallogr. 24:409-411, 1991.
27. Otwinowski, Z. DENZO: An Oscillation Data Processing Program for Macromolecular Crystallography. New Haven, CT: Yale Univ. Press. 1993.
28. Collaborative Computational Project, Number 4. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D50:760-763, 1994.
29. Matthews, B.W. Solvent content of protein crystals. J. Mol. Biol. 33:491-497, 1968.
30. Navaza, J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. A50:157-163, 1994.
31. Jones, T.A., Zou, J.-Y., Cowan, S.W., Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47:110-119, 1991.
32. Bruenger, A.T., Krukowski, A., Erickson, J.W. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallogr. A46:585-593, 1990.
33. Murshudov, G.N., Vagin, A.A., Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53:240-255, 1997.
34. Brünger, A.T. Free R-value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature 355: 472-475, 1992.
35. Hutchinson, E.G., Thornton, J.M. HERA - a program to draw schematic diagrams of protein secondary structures. Proteins 8:203-212, 1990.
36. Kabsch, W., Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637, 1983.
37. Kraulis, J.P. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structure. J. Appl. Crystallogr. 24:946-950, 1991.
38. Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26:283-291, 1993.
39. Engh, R.A., Huber, R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A47:392-400, 1991.
40. Luzzati, V. Traitement statistique des erreurs dans la determination des structures cristallines. Acta Crystallogr. 5:802-810, 1952.
41. Evans, S.V. SETOR: Hardware-lighted three-dimensional solid model representations of macromolecules. J. Mol. Graphics 11:134-138, 1993.
42. Kabsch, W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A32:922-923, 1976.
43. Buchwalder, A., Szadkowski, H., Kirschner, K. A fully active variant of dihydrofolate reductase with a circularly permuted sequence. Biochemistry 31:1621-1630, 1992.
44. Graf, R., Schachman, H.K. Random circular permutation of genes and expressed polypeptide chains: Application of the method to the catalytic chains of aspartate transcarbamoylase. Proc. Natl. Acad. Sci. USA 93:11591-11596, 1996.
45. Malet, C., Jiménez-Barbero, J., Bernabé, M., Brosa, C., Planas, A. Stereochemical course and structure of the products of the enzymic action of endo-1,3-1,4-β-D-glucan 4-glucanohydrolase from Bacillus licheniformis. Biochem. J. 296:753-758, 1993.
46. Welfle, K., Misselwitz, R., Welfle, H., Simon, O., Politz, O., Borriss, R. Microcalorimetric determination of the thermostability of three hybrid (1-3,1-4)-β-glucanases. J. Biomol. Struct. Dyn. 11:1417-1424, 1994.
47. Chantrenne, H. The Biosynthesis of Proteins. New York: Pergamon,1961, pp. 92-125.
48. Shortle, D., Wang, Y., Gillespie, J.R., Wrabl, J.O. Protein folding for realists: A timeless phenomenon. Protein Sci. 5:991-1000, 1996.
49. Alexandrov, N. Structural argument for N-terminal initiation of protein folding. Protein Sci. 2:1989-1992, 1993.
50. Schulz, G.E. A critical evaluation of methods for prediction of protein secondary structures. Annu. Rev. Biophys. Bioeng. 12:183-210, 1988.