A structural basis for transition-state stabilization in antibody-catalyzed hydrolysis: Crystal structures of an abzyme at 1.8 Å resolution

Journal of Molecular Biology

Volumn 281, Issue 3, 1998, Pages 501-511

  Kristensen, Ole ^a   Vassylyev, Dmitry G ^a   Tanaka, Fujie ^a   Morikawa, Kosuke ^a   Fujii, Ikuo ^a  

^a BIOMOL ENG RESEARCH INSTITUTE   (Japan)

Author keywords

Catalytic antibody; Fab; Transition state stabilization; X ray crystallography

Indexed keywords

CATALYTIC ANTIBODY; CHLORAMPHENICOL; HAPTEN; HISTIDINE; OXYGEN;

ANTIBODY AFFINITY; ANTIBODY STRUCTURE; ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DRUG HYDROLYSIS; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING;

FELIS CATUS;

EID: 0032555713     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1940     Document Type: Article

References (45)

1. Arevalo J.H., Hassig C.A., Stura E.A., Sims M.J., Taussig M.J., Wilson I.A. Structural analysis of antibody specificity. detailed comparison of five fab′-steroid complexes. J. Mol. Biol. 241:1994;663-690
2. Bartlett P.A., Marlowe C.K. Evaluation of intrinsic binding energy from a hydrogen bonding group in an enzyme inhibitor. Science. 235:1987;569-571
3. Bash P.A., Singh U.C., Brown F.K., Langridge R., Kollman P.A. Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science. 235:1987;574-576
4. Branden C., Tooze J. Introduction to Protein Structure. 1991;Garland Publishing, Inc, New York
5. Brünger A.T. Extension of molecular replacement A new search strategy based on Patterson correlation refinement. Acta. Crystallog. sect. A. 46:1990;46-57
6. Brünger A.T. X-PLOR, Version 3.1, A System for X-ray Crystallography and NMR. 1992;Yale University Press
7. Burley S.K., Petsko G.A. Aromatic-aromatic interaction a machanism of proten structure stabilization. Science. 229:1985;23-28
8. Chacko S., Silverton E., Kam-Morgan L., Smith-Gill S., Cohen G., Davies D. Structure of an antibody-lysozyme complex Unexpected effect of a conservative mutation. J. Mol. Biol. 245:1995;261-274
9. Charbonnier J.B., Carpenter E., Gigant B., Golinelli-Pimpaneau B., Eshhar Z., Green B.S., Knossow M. Crystal structure of the complex of a catalytic antibody Fab fragment with a transition state analog structural similarities in esterase-like catalytic antibodies. Proc. Natl Acad. Sci. USA. 92:1995;11721-11725
10. Charbonnier J.B., Golinelli-Pimpaneau B., Gigant B., Tawfik D.S., Chap R., Schindler D.G., Kim S.-H., Green B.S., Eshar Z., Knossow M. Structural convergence in the active sites of a family of catalytic antibodies. Science. 275:1997;1140-1142
11. Deslongchamps P. Esters and related functions. Stereoelectronic Effects in Organic Chemistry. 1983;54-100 Pegamon Press, Oxford
12. Fersht A. Ensyme-substrate complementarity and use of binding energy in catalysis. Enzyme Structure and Mechanism. 2nd edit. :1985;311-346 W. H. Freeman and Company, New York
13. Fujii I., Tanaka F., Miyashita H., Tanimura R., Kinoshita K. Correlation between antigen-combining-site structures and functions within a panel of catalytic antibodies generated against a single transition state analog. J. Am. Chem. Soc. 117:1995;6199-6209
14. Golinelli-Pimpaneau B., Gigant B., Bizebard T., Navaza J., Saludjian P., Zemel R., Tawfik D.S., Eshhar Z., Green B.S., Knossow M. Crystal stucture of a catalytic antibody Fab with esterase-like activity. Structure. 2:1994;175-183
15. Guddat L.W., Shan L., Anchin J.M., Linthicum D.S., Edmundson A.B. Local and transmitted conformational changes on complexation of an anti-sweetener Fab. J. Mol. Biol. 236:1994;247-274
16. Guo J., Huang W., Scanlon T.S. Kinetic and mechanistic characterization of an efficient hydrolytic antibody evidence for the formation of an acyl intermediate. J. Am. Chem. Soc. 116:1994;6062-6069
17. Higashi T. The processing of diffraction data taken on a screenless Weissenberg camera for macromolecular crystallography. J. Appl. Crystallog. 22:1989;9-18
18. Jones T.A., Cowan S., Zou J.-Y., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A. 47:1991;110-119
19. Kleywegt G.J., Jones T.A. A super position. ESF/CCP4 Newsletter. 31:1994;9-14
20. Kraulis P.J. MOLSCRIPT a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950
21. Kristensen O., Miyashita H., Vassylyev D.G., Tanaka F., Fujii I., Morikawa K. Crystallization and preliminary X-ray analysis transition state complex of a chloramphenicol prodrug specific catalytic antibody. Protein Pep. Letters. 1:1995;252-255
22. Laskowski R.A., MacArthur M.W., Moss D.J., Thornton J.M. PROCHECK a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291
23. Lerner R.A., Schultz P.G. Antibody catalysis of difficult chemical transformations. Acc. Chem. Res. 26:1993;391-395
24. Lerner R.A., Benkovic S.J., Schultz P.G. At the crossroads of chemistry and immunology catalytic antibodies. Science. 252:1991;659-667
25. MacBeath G., Hilvert D. Hydrolytic antibodies variations on a theme. Chem. Biol. 3:1996;433-445
26. McRee D.E. A visual protein crystallographic software system for X11/Xview. J. Mol. Graphics. 10:1992;44-46
27. Merritt E.A., Murphy M.E.P. Raster3D Version 2.0 - a program for photorealistic molecular graphics. Acta. Crystallog. sect. D. 50:1994;869-873
28. Miyashita H., Karaki Y., Kikuchi M., Fujii I. Prodrug activation via catalytic antibodies. Proc. Natl Acad. Sci. USA. 90:1993;5337-5340
29. Miyashita H., Hara T., Tanimura R., Tanaka F., Kikuchi M., Fujii I. A common ancestry for multiple catalytic antibodies generated against a single transition-state analog. Proc. Natl Acad. Sci. USA. 91:1994;6045-6049
30. Miyashita H., Hara T., Tanimura R., Fukuyama S., Cagnon C., Kohara A., Fujii I. Site-directed mutagenesis of active site contact residues in a hydrolytic abzyme evidence for an essential histidine involved in transition state stabilization. J. Mol. Biol. 267:1997;1247-1257
31. Otwinowski Z. Data Collection and Processing Proceedings of the CCP4 Study Weekend, 29-30 January. 1993;Daresbury Laboratory, Warrington W A4 4AD, UK
32. Padlan E.A. Anatomy of the antibody molecule. Mol. Immunol. 31:1994;169-217
33. Patten P.A., Gray N.S., Yang P.L., Marks C.B., Wedemayer G.J., Boniface J.J., Stevens R.C., Schultz P.G. The immunological evolution of catalysis. Science. 271:1996;1086-1091
34. Schultz P.G., Lerner R.A. From molecular diversity to catalysis lessons from the immune system. Science. 269:1995;1835-1842
35. A Suite of Programs for Protein Crystallography. 1979;Daresbury Laboratory, Warrington W A4 4AD, UK
36. Shokat K.M., Schultz P.G. Catalytic antibodies. Annu. Rev. Immunol. 8:1990;335-363
37. Stanfield R.L., Fieser T.M., Lerner R.A., Wilson I.A. Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2. 8 Å Science. 248:1990;712-719
38. Steigemann W. Die Entwicklung und Anwendung von Rechen-programmen zur Strukturanalyse von Proteinen am Beispiel des Trypsin-Trypsininhibitor Komplexes, des freien Inhibitors und der L-Asparaginase. 1974;PhD, Technical University of Munich, Germany
39. Stewart J.D., Benkovic S.J. Transition-state stabilization as a measure of the efficiency of antibody catalysis. Nature. 375:1995;388-391
40. Tramontano A., Janda K.D., Lerner R.A. Catalytic antibodies. Science. 234:1986;1566-1570
41. Tronrud D.E., Holden H.M., Matthews B.W. Structures of two thermolysin-inhibitor complexes that differ by a single hydrogen bond. Science. 235:1987;571-574
42. Tulip W.R., Varghese J.N., Laver W.G., Webster R.G., Colman P.M. Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab complex. J. Mol. Biol. 227:1992;122-148
43. Wang B.-C. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115:1985;90-112
44. Wedemayer G.J., Wang L.H., Patten P.A., Schultz P.G., Stevens R.C. Crystal structures of the free and liganded form of an esterolytic catalytic antibody. J. Mol. Biol. 268:1997;390-400
45. Zhou G.W., Guo J., Huang W., Fletterick R.J., Scanlan T.S. Crystal structure of a catalytic antibody with a serine protease active site. Science. 265:1994;1059-1064