Bacillus/enzymology/genetics; Bacterial Proteins/genetics/metabolism; Binding Sites; Models, Molecular; Penicillinase/genetics/metabolism; Penicillins/metabolism; Protein Binding; Protein Conformation; X-Ray Diffraction
Abstract :
[en] Two crystal forms (A and B) of the 29,500 Da Class A beta-lactamase (penicillinase) from Bacillus licheniformis 749/C have been examined crystallographically. The structure of B-form crystals has been solved to 2 A resolution, the starting model for which was a 3.5 A structure obtained from A-form crystals. The beta-lactamase has an alpha + beta structure with 11 helices and 5 beta-strands seen also in a penicillin target DD-peptidase of Streptomyces R61. Atomic parameters of the two molecules in the asymmetric unit were refined by simulated annealing at 2.0 A resolution. The R factor is 0.208 for the 27,330 data greater than 3 sigma (F), with water molecules excluded from the model. The catalytic Ser-70 is at the N-terminus of a helix and is within hydrogen bonding distance of conserved Lys-73. Also interacting with the Lys-73 are Asn-132 and the conserved Glu-166, which is on a potentially flexible helix-containing loop. The structure suggests the binding of beta-lactam substrates is facilitated by interactions with Lys-234, Thr-235, and Ala-237 in a conserved beta-strand peptide, which is antiparallel to the beta-lactam's acylamido linkage; an exposed cavity near Asn-170 exists for acylamido substituents. The reactive double bond of clavulanate-type inhibitors may interact with Arg-244 on the fourth beta-strand. A very similar binding site architecture is seen in the DD-peptidase.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Moews, P. C.
Knox, J. R.
Dideberg, O.
Charlier, Paulette ; Université de Liège - ULiège > Département des sciences de la vie > Cristallographie des macromolécules biologiques
Frère, Jean-Marie ; Université de Liège - ULiège > Centre d'ingénierie des protéines
Language :
English
Title :
Beta-lactamase of Bacillus licheniformis 749/C at 2 A resolution.
Publication date :
1990
Journal title :
Proteins
ISSN :
0887-3585
eISSN :
1097-0134
Publisher :
Wiley Liss, Inc., New York, United States - New York
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Bibliography
Kelly J.A., Dideberg O., Charlie P., Wery J.P., Liberrt M., Moews P.C., Knox J.R.C., Fraipont C., Joris B., Dusart J., Frére J.‐M., Ghuysen J.M. (1986) On the origin of bacterial resistance to penicillin: Comparison of a β‐lactamase and a penicillin target. Science 231:1429-1431.
Coulson (1985) β‐Lactamases: Molecular studies. Biotechnol. Gen. Eng. Rev. 3:219-253.
Frére J.‐M., Joris B. (1985) Penicillin‐sensitive enzymes in peptidoglycan biosynthesis. CRC Crit. Rev. Microbiol. 11:299-396.
Fink A.L., The molecular basis of β‐lactamase catalysis and inhibition. Pharma. Res.; 1985, 55-96.
Knowles J.R. (1985) Penicillin resistance: The chemistry of β‐lactamase inhibition. Accts. Chem. Res. 18:97-102.
Pratt R.F. (1988) β‐lactamase inhibitors. Design of Enzyme Inhibitors as Drugs , Sandler, M., Smith., H. J., Oxford University Press; 178-205.
Herzeberg O., Moult J. (1987) Bacterial resistance to β‐lactam antibiotics: Crystal Structure of β‐lactamase from Staphylococcus aureus PC1 at 2.5 Å resolution. Science 236:694-701.
Dideberg O., Charlie P., Wery J.‐P., Dehottay P., Dursart J., Erpicum Y., Frére J.‐M., Ghuysen J.‐M. (1987) The crystal structure of te β‐lactamase of Streptomyces albus G at 0.3 nm resolution. Biochem. J. 245:911-913.
Knox J.R., Kelly J.A., Moews P.C., Murthy N.S. (1976) 5.5 Å crystallographic structure of penicillin β‐lactamase and radius of gyration in solution. J. Mol. Biol. 104:865-875.
Charlie P., Dideberg O., Frére J.‐M., Moews P.C., Knox J.R. (1983) Crystallographic data for the β‐lactamase from Enterobacter cloacae P99. Journal of Molecular Biology 171:237-238.
Samraoui B., Sutton B.J., Todd R.J., Artymiuk P.J., Waley S.G., Phillips D.C., Waley S.G., Phillips D.C. (1986) Tertiary structural similarity between a class A β‐lactamase and a penicillin‐sensitive D‐alanyl carboxypeptidase‐transpeptidase. Nature (London) 320:378-380.
Sutton B.J., Artymiuk P.J., Cordero‐Borboa A.E., Little C., Phillips D.C., Waley S.G. (1987) An X‐ray‐crystallographic study of β‐lactamase II from Bacillus cereus at 0.35 nm resolution. Biochem. J. 248:181-188.
Joris B., Ghusyn J.M., Drive G., Renard A., Dideberg O., Charlie P., FréRe J.‐M., Kelly J.A., Boyington J.C., Moews P.C., Konx J.R. (1988) The active‐site‐serine penicillin recognizing enzymes as members of the Streptomyces R61 DD‐peptidase family. Biochem. J. 250:313-324.
Wang B.C. (1985) Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol 115:90-111.
Kelly J.A., Knox J.R., Moews P.C., Hite G.J., Bartolone J.B., Zhao H., Joris B., Frére J.‐M., Ghuysen J.‐M. (1985) 2.8 Å Structure of pencillin‐0sensitive D‐alanyl carboxypetidase‐transpeptidase from Streptomyces R61 and complexes with β‐lactams. J. Biol. Chem. 260:6449-6458.
Kelly J.A., Knox J.R., Zhao H., Frére J.‐M., Ghuysen J.M. (1989) Crystallographic mapping of β‐lactams bound to a DD‐peptidase. J. Mol. Biol. 209:281-295.
Neugebauer K., Sprengel R., Schaller H. (1981) Penicillinase from Bacillus licheniformis: Nucleotide sequences of the gene and implication for the biosynthesis of a secretary protein in a Gram‐positive bacterium. Nucl. Acids. Res. 9:2577-2588.
Dideberg O., Libert M., Frére J.‐M., Charlie P., Zhao H.C., Knox J.R. (1985) Crystallization and preliminary x‐ray data for the exocellular β‐lactamase of Bacillus licheniformis 749/C. J. Mol. Biol 181:145-146.
North A.C.T., Phillips D.C., Mathews F.S. (1968) A semi‐empirical method of absorption correction. Acta Crystallographica Section A 24 A:351-359.
Blow D.M., Crick F.H.C. (1959) The treatment of errors in the isomorphous replacement method. Acta Crystallographica 12:794-802.
Williams T.V., A man‐machine interface for interpreting electron density maps. Ph.D. Dissertation. University of North Carolina; 1982.
Sobottka S.E., Cornick G.C., Kretsinger R.H., Rains R.G., Stephens W.A., Weissman L.J. (1984) A MWPX X‐ray diffractometer facility for protein crystallography. Nucl. Inst. Methods. 220:575-581.
Crowther R.A. (1972) The fast rotation function. The Molecular Replacement Methods , Rossmann, M. G., Int. Sci. Rev. Ser., No. 13, New York, Gordon & Breach; 173-178.
Fujinaga M., Read R.J. (1987) Experiences with a new translation function program. Journal of Applied Crystallography 20:517-521.
Stewart J.M., Kruger G.J., Ammon, Dickinson C., Hall S.R., The x‐ray system of crystallographic programs. Technical Report TR‐192, University of Maryland; 1972.
Adams M.J., Haas D.J., Jeffrey B.A., McPherson A., Mermall H.L., Rossmann J., Schevitz R.W., Wonacott A.J. (1981) Low resolution study of L lactase dehydrogenase. J. Mol. Biol. 41:159-188.
Jones T.A. (1982) FRODO: a graphics fitting program for macromolecules. conformational Crystallography , D. Sayre, Oxford, Clarendon Press; 303-317.
Brunger A.T. (1989) A memory‐efficient fast Fourier transformation algorithm for crystallographic refinement on super‐computers. Acta Crystallographica Section A Foundations of Crystallography 45 A:42-50.
Brünger A.T., Karplus M., Petsko G.A. (1989) Crystallographic refinement by simulated annealing: Application to crambin. Acta Crystallographica Section A Foundations of Crystallography 45 A:50-61.
Brünger A.T., X‐PLOR (Version 1.5) Manual The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University.; 1988.
Read R.J. (1988) Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystalogr 42 A:140-149.
Baht T.N. (1988) Calculation of an OMIT map. Journal of Applied Crystallography 21:279-281.
Baker E.N. (1988) Structure of azurin from Alcaligenes denitrifications. Refinement at 1.8Å resolution and comparison of the two crystallographically independent molecules. J. Mol. Biol. 203:1071-1095.
Killy J.A., Boyington J.C., Moews P.C., Knox J.R., Dideberg B., Dusart J., Frère J.‐M., Ghuysen J.M. (1987) Crystallographic comparisons of penicillin‐binding enzymes and studies of antibiotic binding. Frontiers of Antibiotic Research, Takeda science Foundation , Umesawa, H., New York, Academic Press; 64-82.
Knox J.R., Kelly J.A., Moews P.C., Zhao H., Moring J., Rao J.K.M., Boyington J., Dideberg O., Charlier P., Libert M. (1987) Crystallography of penicillin‐binding enzymes. Three‐dimensional Structure and Drug Action , Iitaka, I., Itai, A., Tokyo, University of Tokyo Press; 64-82.
Chou P.Y., Fasman G.D. (1977) β‐Turns in proteins. J. Mol. Biol. 115:135-175.
Garnier J., Osguthorpe D.J., Robson R. (1978) Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular protein. J. Mol. Biol. 120:97-120.
Moews P.C., Knox J.R. (1979) Predicted secondary structures of four penicillin β‐lactamases and a comparison with two lysozymes. Int. J. Pept. Protein Res. 13:385-393.
Pain R.H., Virdin R. (1979) The structural and conformational basis of β‐lactamase activities. β‐Lactamases , Hamilton‐Miller, J. M. T., Smith, J. T., London, Academic Press; 141-181.
Bunster M., Cid H. (1984) A model for the secondary structure of β‐lactamases. FEBS Lett. 175:267-274.
Ambler R.P. (1980) The structure of β‐lactamases. Phil. Trans Ry. Soc. London, Ser. B 289:321-331.
Coulson A., Fourth β‐Lactamase Workshop, Holy Island, UK; 1988.
Murthy N.S., Braswell E.H., Knox J.R. (1978) The association behavior of β‐lactamases in polyethylene glycol solutions. Biopolymers 27:865-881.
Richardson J.S. (1981) The anatomy and taxonomy of protein folding. Adv. Prot. Chem. 34:167-339.
Medgwick P.J., Waley S.G. (1987) β‐Lactamase I from Bacillus cereus: Structure and site‐directed mutagenesis. Biochemical Journal 248:657-662.
Hall A., Knowles J.R. (1976) Directed selective pressure on a β‐lactamase to analyze molecular changes involved in development of enzyme function. Nature (London) 264:803-804.
Little G., Emanuael E.L., Gangnon J., Waley S.G. (1986) Carboxy groups as essential residues in β‐lactamases. Biochem. J. 240:215-219.
Kraut J. (1977) Serine proteases: Structure and mechanism of catalysis. Annu. Rev. Biochem. 46:331-359.
Boyd D.B. (1982) Theoretical and physiochemical studies on β‐lactam antibiotics. Chemistry and Biology of β‐lactam antibiotics , Morin, R. B., Gorman, M., New York, Academic Press; 1:437-545.
Boyd D.B. (1987) Computers‐assisted molecular design studies of β‐lactam antibiotics. Frontiers of Antibiotic Research , New York, Academic press; 339-356.
Varetto L., Frère J.‐M., Ghuysen J.M. (1987) The importance of the negative charge of β‐lactam compounds for the inactivation of the active‐site serine DD‐peptidase of Streptomyces R61. FEBS Lett. 225:218-222.
Pollock M.R. (1968) Range and significance of variations among bacterial penicillinases. Ann. N. Y. Acad. Sci. 151:502-515.
Citri N., Pollock M.R. (1966) The biochemistry and function of β‐lactamase (penicillinase). Adv. Enzymol. 28:237-324.
Naylor J.H.C. (1971) Structure‐activity relationships in semisynthetic penicillins. Proceedings of the Royal Society B: Biological Sciences 179:357-367.
Hol W.G.J. (1985) The role of the α‐helix dipole in protein function and structure. Prog. Biophys. Mol. Biol. 45:149-195.
Drenth J., Kalk K.H., Swen H.M. (1976) Binding of chloromethyl kton substrate analogues to crystalline papain. Biochemistry 15:3731-3738.
Lowe G., Swain S. Do β‐lactam antibiotics , London, Royal Society of Chemistry; 1985, 209-221.
Jones M., Buckwell S.C., Page M.I., Wigglesworth R. A reversible inhibitor of β‐lactamase I from Bacillus cereus. J. Chem. Soc. Chem. Commun. 1989:70-71.
Frère J.‐M., Dormans C., Lanzini V.M., Duyckaerts C. (1982) Interaction of clavulanate with the β‐lactamases of Streptomyces albus G and Actinomadura R39. Biochem. J. 207:429-436.
Knox J.R., Kelly J.A. (1989) Crystallographic comparison of penicillin‐recognizing enzymes. Molecular Recognition: Chemical and Biochemical Problem , Roberts, S., Royal Soc. Chem.; 46-55.
Pollock M.R. (1965) Purification and properties of penicillinases from two strains of Bacillus licheniformis: A chemical, physiochemical and physiological comparison. Biochem. J. 94:666-675.
Fink A.L., Ellerby L.M., Escobar W.A., Mitchinson C., Wells J.A., Site‐directed mutagenesis studies on the role of lysine‐234 in β‐lactamase catalysis. Submitted.; .
Philipon A., Labia R., Jacoby G. (1989) Extended‐spectrum β‐lactamases. Antimicrobial Agents and Chemotherapy 33:1131-1136.
Dalbadie‐McFarland G., Cohen L.W., Riggs A.D., Morin C., Itakura K., Richards J.H. (1982) Oligonucleotide‐directed mutagenesis as a general and powerful method for studies of protein function. Proceedings of the National Academy of Sciences 79:6409-6413.
Schultz S.C., Richards J.H. (1986) Site‐saturation studies of β‐lactamase: Production and characterization of mutant β‐lactamases with all possible amino acid substitutions at residue 71. Proc. Natl. Acad. Sci. U.S.A. 83:1588-1592.
Oliphant A., Struhl L., Creating novel β‐lactamases by random selection. Proc. Natl. Acad. Sci. U.S.A. In press.; .
Oefner C., Fourth β‐Lactamase Workshop, Holy Island, UK; 1988.
Christenson J.G., Pruess D.L., Talbot M., Keith D.D. (1988) Antibacterial properties of (2,3)‐α‐ and (2,3)‐β‐methylene analogs of penicillin G. Antimicrob. Ag. Chemother. 32:1005-1011.
Dexter D.D., van der Veen J.M. Conformations of penicillin G. J. Chem. Soc. Perkin I. 1978:185-190.
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