51
|
Spencer J, Read J, Sessions RB, Howell S, Blackburn GM, Gamblin SJ. Antibiotic recognition by binuclear metallo-beta-lactamases revealed by X-ray crystallography. J Am Chem Soc 2006; 127:14439-44. [PMID: 16218639 DOI: 10.1021/ja0536062] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metallo-beta-lactamases are zinc-dependent enzymes responsible for resistance to beta-lactam antibiotics in a variety of host bacteria, usually Gram-negative species that act as opportunist pathogens. They hydrolyze all classes of beta-lactam antibiotics, including carbapenems, and escape the action of available beta-lactamase inhibitors. Efforts to develop effective inhibitors have been hampered by the lack of structural information regarding how these enzymes recognize and turn over beta-lactam substrates. We report here the crystal structure of the Stenotrophomonas maltophilia L1 enzyme in complex with the hydrolysis product of the 7alpha-methoxyoxacephem, moxalactam. The on-enzyme complex is a 3'-exo-methylene species generated by elimination of the 1-methyltetrazolyl-5-thiolate anion from the 3'-methyl group. Moxalactam binding to L1 involves direct interaction of the two active site zinc ions with the beta-lactam amide and C4 carboxylate, groups that are common to all beta-lactam substrates. The 7beta-[(4-hydroxyphenyl)malonyl]-amino substituent makes limited hydrophobic and hydrogen bonding contacts with the active site groove. The mode of binding provides strong evidence that a water molecule situated between the two metal ions is the most likely nucleophile in the hydrolytic reaction. These data suggest a reaction mechanism for metallo-beta-lactamases in which both metal ions contribute to catalysis by activating the bridging water/hydroxide nucleophile, polarizing the substrate amide bond for attack and stabilizing anionic nitrogen intermediates. The structure illustrates how a binuclear zinc site confers upon metallo-beta-lactamases the ability both to recognize and efficiently hydrolyze a wide variety of beta-lactam substrates.
Collapse
Affiliation(s)
- James Spencer
- Departments of Cellular and Molecular Medicine and Biochemistry, University of Bristol School of Medical Sciences, University Walk, Bristol BS8 1TD, United Kingdom
| | | | | | | | | | | |
Collapse
|
52
|
Breyfogle LE, Williams CK, Young VG, Hillmyer MA, Tolman WB. Comparison of structurally analogous Zn2, Co2, and Mg2catalysts for the polymerization of cyclic esters. Dalton Trans 2006:928-36. [PMID: 16462953 DOI: 10.1039/b507014g] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three dimetallic monoethoxide complexes supported by a binucleating phenoxide ligand, LM2Cl2OEt (M = Zn, Co, or Mg), were prepared and shown by X-ray crystallography to be structurally analogous. Comparative studies of their cyclic ester polymerization reactivity revealed different trends for reactions with epsilon-caprolactone and lactide, however, implicating complicated effects of metal ion variation in these polymerizations.
Collapse
Affiliation(s)
- Laurie E Breyfogle
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA
| | | | | | | | | |
Collapse
|
53
|
Xu D, Zhou Y, Xie D, Guo H. Antibiotic binding to monozinc CphA beta-lactamase from Aeromonas hydropila: quantum mechanical/molecular mechanical and density functional theory studies. J Med Chem 2005; 48:6679-89. [PMID: 16220984 DOI: 10.1021/jm0505112] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The active-site dynamics of apo CphA beta-lactamase from Aeromonas hydropila and its complex with a beta-lactam antibiotic molecule (biapenem) are simulated using a quantum mechanical/molecular mechanical (QM/MM) method and density functional theory (DFT). The quantum region in the QM/MM simulations, which includes the Zn(II) ion and its ligands, the antibiotic molecule, the catalytic water, and an active-site histidine residue, was treated using the self-consistent charge density functional tight binding (SCC-DFTB) model. Biapenem is docked at the active site unambiguously, based on a recent X-ray structure of an enzyme-intermediate complex. The substrate is found to form the fourth ligand of the zinc ion with its 3-carboxylate oxygen and to hydrogen bond with several active-site residues. The stability of the metal-ligand bonds and the hydrogen-bond network is confirmed by 500 ps molecular dynamics simulations of both the apo enzyme and the substrate-enzyme complex. The structure and dynamics of the substrate-enzyme complex provide valuable insights into the mode of catalysis in such enzymes that is central to the bacterial resistance to beta-lactam antibiotics.
Collapse
Affiliation(s)
- Dingguo Xu
- Department of Chemistry, University of New Mexico, Albuquerque, NM 87131, USA
| | | | | | | |
Collapse
|
54
|
Weston J. Mode of action of bi- and trinuclear zinc hydrolases and their synthetic analogues. Chem Rev 2005; 105:2151-74. [PMID: 15941211 DOI: 10.1021/cr020057z] [Citation(s) in RCA: 272] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jennie Weston
- Institut für Organische und Makromolekulare Chemie, Friedrich-Schiller-Universität, Jena, Germany.
| |
Collapse
|
55
|
Oelschlaeger P, Mayo SL. Hydroxyl Groups in the ββ Sandwich of Metallo-β-lactamases Favor Enzyme Activity: A Computational Protein Design Study. J Mol Biol 2005; 350:395-401. [PMID: 15946681 DOI: 10.1016/j.jmb.2005.04.044] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Accepted: 04/21/2005] [Indexed: 11/23/2022]
Abstract
Metallo-beta-lactamases challenge antimicrobial therapies by their ability to hydrolyze and inactivate a broad spectrum of beta-lactam antibiotics. The potential of these enzymes to acquire enhanced catalytic efficiency through mutation is of great concern. Here, we explore the potential of computational protein design to predict mutants of the imipenemase IMP-1 that modulate the catalytic efficiency of the enzyme against a range of substrates. Focusing on the four amino acid positions 69, 121, 218, and 262, we carried out a number of design calculations. Two mutant enzymes were predicted: the single mutant S262A and the double mutant F218Y-S262A. Compared to IMP-1, the single mutant (S262A) results in the loss of a hydroxyl group and the double mutant (F218Y-S262A) results in a hydroxyl transfer from position 262 to position 218. The presence of both hydroxyl groups at positions 218 and 262 was tested by examining the mutant F218Y. Kinetic constants of IMP-1, the two computationally designed mutants (S262A and F218Y-S262A), and the hydroxyl addition mutant (F218Y) were determined with seven substrates. Catalytic efficiencies are highest for the enzyme with both hydroxyl groups (F218Y) and lowest for the enzyme lacking both hydroxyl groups (S262A). The catalytic efficiencies of the two enzymes with one hydroxyl group each are intermediate, with the F218Y-S262A double mutant exhibiting enhanced hydrolysis of nitrocefin, cephalothin, and cefotaxime relative to IMP-1.
Collapse
Affiliation(s)
- Peter Oelschlaeger
- Division of Biology, California Institute of Technology, Mail Code 114-96, Pasadena, CA 91125, USA
| | | |
Collapse
|
56
|
Park H, Brothers EN, Merz KM. Hybrid QM/MM and DFT investigations of the catalytic mechanism and inhibition of the dinuclear zinc metallo-beta-lactamase CcrA from Bacteroides fragilis. J Am Chem Soc 2005; 127:4232-41. [PMID: 15783205 DOI: 10.1021/ja042607b] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Based on hybrid QM/MM molecular dynamics simulation and density functional theoretical (DFT) calculations, we investigate the mechanistic and energetic features of the catalytic action of dizinc metallo-beta-lactamase CcrA from Bacteroides fragilis. The 200 ps QM/MM simulation of the CcrA enzyme in complex with nitrocefin shows that the substrate beta-lactam moiety is directed toward the active site dizinc center through the interactions of aminocarbonyl and carboxylate groups with the two active site zinc ions and the two conserved residues, Lys167 and Asn176. From the determination of the potential energy profile of a relevant enzymatic reaction model, it is found that the nucleophilic displacement reaction step proceeds with a low-barrier height, leading to the formation of an energetically favored reaction intermediate. The results also show that the high catalytic activity of the CcrA enzyme stems from a simultaneous operation of three catalytic components: activation of the bridging hydroxide nucleophile by zinc-coordinated Asp86; polarization of the substrate aminocarbonyl group by the first zinc ion; stabilization of the negative charge developed on the departing amide nitrogen by the second zinc ion. Consistent with the previous experimental finding that the proton-transfer reaction step is rate-limiting, the activation energy of the second step is found to be 1.6 kcal/mol higher than that of the first step. Finally, through an examination of the structural and energetic features of binding of a thiazolidinecarboxylic acid inhibitor to the active site dizinc center, a two-step inhibition mechanism involving a protonation-induced ligand exchange reaction is proposed for the inhibitory action of a tight-binding inhibitor possessing a thiol group.
Collapse
Affiliation(s)
- Hwangseo Park
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802-6300, USA
| | | | | |
Collapse
|
57
|
Walsh TR, Toleman MA, Poirel L, Nordmann P. Metallo-beta-lactamases: the quiet before the storm? Clin Microbiol Rev 2005; 18:306-25. [PMID: 15831827 PMCID: PMC1082798 DOI: 10.1128/cmr.18.2.306-325.2005] [Citation(s) in RCA: 999] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ascendancy of metallo-beta-lactamases within the clinical sector, while not ubiquitous, has nonetheless been dramatic; some reports indicate that nearly 30% of imipenem-resistant Pseudomonas aeruginosa strains possess a metallo-beta-lactamase. Acquisition of a metallo-beta-lactamase gene will invariably mediate broad-spectrum beta-lactam resistance in P. aeruginosa, but the level of in vitro resistance in Acinetobacter spp. and Enterobacteriaceae is less dependable. Their clinical significance is further embellished by their ability to hydrolyze all beta-lactams and by the fact that there is currently no clinical inhibitor, nor is there likely to be for the foreseeable future. The genes encoding metallo-beta-lactamases are often procured by class 1 (sometimes class 3) integrons, which, in turn, are embedded in transposons, resulting in a highly transmissible genetic apparatus. Moreover, other gene cassettes within the integrons often confer resistance to aminoglycosides, precluding their use as an alternative treatment. Thus far, the metallo-beta-lactamases encoded on transferable genes include IMP, VIM, SPM, and GIM and have been reported from 28 countries. Their rapid dissemination is worrisome and necessitates the implementation of not just surveillance studies but also metallo-beta-lactamase inhibitor studies securing the longevity of important anti-infectives.
Collapse
Affiliation(s)
- Timothy R Walsh
- Department of Pathology and Microbiology, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom.
| | | | | | | |
Collapse
|
58
|
Park H, Merz KM. Force field design and molecular dynamics simulations of the carbapenem- and cephamycin-resistant dinuclear zinc metallo-beta-lactamase from Bacteroides fragilis and its complex with a biphenyl tetrazole inhibitor. J Med Chem 2005; 48:1630-7. [PMID: 15743204 DOI: 10.1021/jm0491290] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of molecular dynamics simulations, we investigate the dynamic properties of the carbapenem- and cephamycin-resistant dinuclear zinc metallo-beta-lactamase from Bacteroides fragilis and its complex with a biphenyl tetrazole inhibitor, 2-butyl-6-hydroxy-3-[2'-(1H-tetrazol-5-yl)biphenyl-4-ylmethyl]-3H-quinazolin-4-one 1 (L-159061). The results obtained with the newly developed force field parameters for the coordination environment of the catalytic zinc ions show that the active site gorge comprising major and minor loops gets deeper and narrower upon binding of the inhibitor, which supports the previous experimental implication that the structural flexibility of the loop structures plays a significant role in enzymatic action. In the presence of the inhibitor, the Trp32 side chain at the apex of the major loop covers the entrance of active site channel, thereby contributing to the stabilization of the enzyme-inhibitor complex. In addition to a direct coordination of the inhibitor tetrazole ring to the second zinc ion in the active site, the hydrogen bonding of Lys167 to the inhibitor carbonyl group and hydrophobic interactions between the inhibitor and side chains of loop residues prove to be significant binding forces of the enzyme-inhibitor complex.
Collapse
Affiliation(s)
- Hwangseo Park
- Department of Chemistry, Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802-6300, USA
| | | |
Collapse
|
59
|
Yamaguchi Y, Kuroki T, Yasuzawa H, Higashi T, Jin W, Kawanami A, Yamagata Y, Arakawa Y, Goto M, Kurosaki H. Probing the role of Asp-120(81) of metallo-beta-lactamase (IMP-1) by site-directed mutagenesis, kinetic studies, and X-ray crystallography. J Biol Chem 2005; 280:20824-32. [PMID: 15788415 DOI: 10.1074/jbc.m414314200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Metallo-beta-lactamase IMP-1 is a di-Zn(II) metalloenzyme that efficiently hydrolyzes beta-lactam antibiotics. Wild-type (WT) IMP-1 has a conserved Asp-120(81) in the active site, which plays an important role in catalysis. To probe the catalytic role of Asp-120(81) in IMP-1, the IMP-1 mutants, D120(81)A and D120(81)E, were prepared by site-directed mutagenesis, and various kinetics studies were conducted. The IMP-1 mutants exhibited 10(2)-10(4)-fold drops in k(cat) values compared with WT despite the fact that they contained two Zn(II) ions in the active site. To evaluate the acid-base characteristics of Asp-120(81), the pH dependence for hydrolysis was examined by stopped-flow studies. No observable pK(a) values between pH 5 and 9 were found for WT and D120(81)A. The rapid mixing of equimolar amounts of nitrocefin and all enzymes failed to result in the detection of an anion intermediate of nitrocefin at 650 nm. These results suggest that Asp-120(81) of IMP-1 is not a factor in decreasing the pK(a) for the water bridging two Zn(II) ions and is not a proton donor to the anionic intermediate. In the case of D120(81)E, the nitrocefin hydrolysis product, which shows a maximum absorption at 460 nm, was bound to D120(81)E in the protonated form. The three-dimensional structures of D120(81)A and D120(81)E were also determined at 2.0 and 3.0 A resolutions, respectively. In the case of D120(81)E, the Zn-Zn distance was increased by 0.3 A compared with WT, due to the change in the coordination mode of Glu-120(81)OE1 and the positional shift in the conserved His-263(197) at the active site.
Collapse
Affiliation(s)
- Yoshihiro Yamaguchi
- Department of Structure-Function Physical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Kumamoto 862-0973, Japan.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
60
|
Crawford PA, Sharma N, Chandrasekar S, Sigdel T, Walsh TR, Spencer J, Crowder MW. Over-expression, purification, and characterization of metallo-beta-lactamase ImiS from Aeromonas veronii bv. sobria. Protein Expr Purif 2005; 36:272-9. [PMID: 15249050 DOI: 10.1016/j.pep.2004.04.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Revised: 04/14/2004] [Indexed: 10/26/2022]
Abstract
The gene from Aeromonas veronii bv. sobria encoding the metallo-beta-lactamase ImiS was subcloned into pET-26b, and ImiS was over-expressed in BL21(DE3) Escherichia coli and purified using SP-Sepharose chromatography. This protocol yielded over 5 mg of ImiS per liter of growth culture under optimum conditions. The biochemical properties of recombinant ImiS were compared with those of native ImiS. Recombinant and native ImiS have the same N-terminus of A-G-M-S-L, and CD spectroscopy was used to show that the enzymes have similar secondary structures. Gel filtration chromatography revealed that both enzymes exist as monomers in solution. MALDI-TOF mass spectra showed that the enzymes have a molecular mass of 25,247 Da, and metal analyses demonstrated that both as-isolated enzymes bind ca. 0.7 mol of Zn(II). Metal titrations demonstrate that the maximum activity of recombinant ImiS occurs when the enzyme binds one equivalent of zinc. Steady-state kinetic studies reveal that recombinant ImiS is a carbapenemase like native ImiS and that the recombinant enzyme exhibits similar kcat and K(m) values for the substrates tested, as compared to the native enzyme. This over-expression protocol now allows for detailed spectroscopic and mechanistic studies on ImiS as well as site-directed mutants of ImiS to be prepared for future structure/function studies.
Collapse
Affiliation(s)
- Patrick A Crawford
- Department of Chemistry and Biochemistry, 112 Hughes Hall, Miami University, Oxford, OH 45056, USA
| | | | | | | | | | | | | |
Collapse
|
61
|
Rasia RM, Vila AJ. Structural determinants of substrate binding to Bacillus cereus metallo-beta-lactamase. J Biol Chem 2004; 279:26046-51. [PMID: 15140877 DOI: 10.1074/jbc.m311373200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Binding and hydrolysis of the beta-lactams cefotaxime, cephapirin, imipenem, and benzylpenicillin by the metallo-beta-lactamase from Bacillus cereus were studied by presteady state kinetic measurements. In all cases, the substrate was unmodified in the most populated reaction intermediate, and no chemically modified substrate species accumulated to a detectable amount. The cephalosporins tested showed similar formation rate constants for this intermediate, and they differed mostly in their decay rates. Formation of a non-productive enzyme.substrate complex was detected for imipenem. The substrate binding differences can be accounted for by considering the structural features of each substrate. The apoenzyme could not bind any of the substrates, but binding was restored when the apoenzyme was reconstituted with Zn(II), revealing that the metal ions are the main determinants of substrate binding. This evidence is in line with the lack of an optimized substrate recognition patch in B1 and B3 metallo-beta-lactamases that provides a broad substrate spectrum.
Collapse
Affiliation(s)
- Rodolfo M Rasia
- Area Biofisica and Instituto de Biologia Molecular y Celular de Rosario, Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina
| | | |
Collapse
|
62
|
Montoya-Pelaez PJ, Gibson GTT, Neverov AA, Brown RS. La3+-Catalyzed Methanolysis ofN-Aryl-β-lactams and Nitrocefin. Inorg Chem 2003; 42:8624-32. [PMID: 14686838 DOI: 10.1021/ic0302736] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The kinetics of the La(3+)-catalyzed methanolysis of N-phenyl-beta-lactam (2) and N-p-nitrophenyl-beta-lactam (3) as well as that of nitrocefin (1) were studied at 25 degrees C under buffered conditions. In the case of 2 and 3, the observed second-order rate constants (k(2)(obs)) for catalysis plateau at pH 7.5-7.8, reaching values of 1 x 10(-)(2) and 35 x 10(-)(2) M(-)(1) s(-)(1) respectively. Potentiometric titrations of solutions of 2 x 10(-)(3) M La(OTf)(3) were analyzed in terms of a dimer model (La(3+)(2)((-)OCH(3))(n)()), where the number of methoxides varies from 1 to 5. The species responsible for catalysis in the pH range investigated contain 1-3 methoxides, the one having the highest catalytic activity being La(3+)(2)((-)OCH(3))(2), which comprises 80% of the total La(3+) forms present at its pH maximum of 8.9. The catalysis afforded by the La(3+) dimers at a neutral pH is impressive relative to the methoxide reactions: at pH 8.4 a 1 mM solution of catalyst (generated from 2 mM La(OTf)(3)) accelerated the methanolysis of 2 by approximately 2 x 10(7)-fold and 3 by approximately 5 x 10(5)-fold. As a function of metal ion concentration, the La(3+)-catalyzed methanolysis of 1 proceeds by pathways involving first one bound metal ion and then a second La(3+) leading to a plateau in the k(obs) vs [La(3+)](total) plots at all pH values. The k(max)(obs) pseudo-first-order rate constants at the plateaus, representing the spontaneous methanolysis of La(3+)(2)(1(-)) forms, has a linear dependence on [(-)OCH(3)] (slope = 0.84 +/- 0.05 if all pH values are used and 1.02 +/- 0.03 if all but the two highest pH values are used). The speciation of bound 1 at a La(3+) concentrations corresponding to that of the onset of the kinetic plateau region was approximated through potentiometric titration of the nonreactive 3,5-dinitrobenzoic acid in the presence of 2 equiv of La(OTf)(3). A total speciation diagram for all bound forms of La(3+)(2)(1(-))((-)OCH(3))(n)(), where n = 0-5, was constructed and used to determine their kinetic contributions to the overall pH vs k(max)(obs) plot under kinetic conditions. Two kinetically equivalent mechanisms were analyzed: methoxide attack on La(3+)(2)(1(-))((-)OCH(3))(n)(), n = 0-2; unimolecular decomposition of the forms La(3+)(2)(1(-))((-)OCH(3))(n)(), n = 1-3.
Collapse
|
63
|
Garrity JD, Carenbauer AL, Herron LR, Crowder MW. Metal binding Asp-120 in metallo-beta-lactamase L1 from Stenotrophomonas maltophilia plays a crucial role in catalysis. J Biol Chem 2003; 279:920-7. [PMID: 14573595 DOI: 10.1074/jbc.m309852200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Metallo-beta-lactamase L1 from Stenotrophomonas maltophilia is a dinuclear Zn(II) enzyme that contains a metal-binding aspartic acid in a position to potentially play an important role in catalysis. The presence of this metal-binding aspartic acid appears to be common to most dinuclear, metal-containing, hydrolytic enzymes; particularly those with a beta-lactamase fold. In an effort to probe the catalytic and metal-binding role of Asp-120 in L1, three site-directed mutants (D120C, D120N, and D120S) were prepared and characterized using metal analyses, circular dichroism spectroscopy, and presteady-state and steady-state kinetics. The D120C, D120N, and D120S mutants were shown to bind 1.6 +/- 0.2, 1.8 +/- 0.2, and 1.1 +/- 0.2 mol of Zn(II) per monomer, respectively. The mutants exhibited 10- to 1000-fold drops in kcat values as compared with wild-type L1, and a general trend of activity, wild-type > D120N > D120C and D120S, was observed for all substrates tested. Solvent isotope and pH dependence studies indicate one or more protons in flight, with pKa values outside the range of pH 5-10 (except D120N), during a rate-limiting step for all the enzymes. These data demonstrate that Asp-120 is crucial for L1 to bind its full complement of Zn(II) and subsequently for proper substrate binding to the enzyme. This work also confirms that Asp-120 plays a significant role in catalysis, presumably via hydrogen bonding with water, assisting in formation of the bridging hydroxide/water, and a rate-limiting proton transfer in the hydrolysis reaction.
Collapse
Affiliation(s)
- James D Garrity
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA
| | | | | | | |
Collapse
|
64
|
Moali C, Anne C, Lamotte-Brasseur J, Groslambert S, Devreese B, Van Beeumen J, Galleni M, Frère JM. Analysis of the importance of the metallo-beta-lactamase active site loop in substrate binding and catalysis. CHEMISTRY & BIOLOGY 2003; 10:319-29. [PMID: 12725860 DOI: 10.1016/s1074-5521(03)00070-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of the mobile loop comprising residues 60-66 in metallo-beta-lactamases has been studied by site-directed mutagenesis, determination of kinetic parameters for six substrates and two inhibitors, pre-steady-state characterization of the interaction with chromogenic nitrocefin, and molecular modeling. The W64A mutation was performed in IMP-1 and BcII (after replacement of the BcII 60-66 peptide by that of IMP-1) and always resulted in increased K(i) and K(m) and decreased k(cat)/K(m) values, an effect reinforced by complete deletion of the loop. k(cat) values were, by contrast, much more diversely affected, indicating that the loop does not systematically favor the best relative positioning of substrate and enzyme catalytic groups. The hydrophobic nature of the ligand is also crucial to strong interactions with the loop, since imipenem was almost insensitive to loop modifications.
Collapse
Affiliation(s)
- Catherine Moali
- Centre d'Ingénierie des Protéines, Université de Liège, Sart-Tilman, B-4000 Liege, Belgium
| | | | | | | | | | | | | | | |
Collapse
|
65
|
Olsen L, Antony J, Ryde U, Adolph HW, Hemmingsen L. Lactam Hydrolysis Catalyzed by Mononuclear Metallo-β-lactamases: A Density Functional Study. J Phys Chem B 2003. [DOI: 10.1021/jp0275950] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lars Olsen
- Department of Mathematics and Physics, The Royal Veterinary and Agricultural University, 1871 Frederiksberg C, Denmark
| | - Jens Antony
- Department of Mathematics and Computer Science, Free University of Berlin, Arnimallee 2-6, D-14195, Germany
| | - Ulf Ryde
- Department of Theoretical Chemistry, University of Lund, Chemical Center, P.O.B. 124, S-221 00 Lund, Sweden
| | - Hans-Werner Adolph
- Center for Bioinformatics, University of the Saarland and Max-Planck-Institut for Informatics, D-66041 Saarbrücken, Germany
| | - Lars Hemmingsen
- Department of Physics, The Quantum Protein Centre, The Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
66
|
Simm AM, Higgins CS, Carenbauer AL, Crowder MW, Bateson JH, Bennett PM, Clarke AR, Halford SE, Walsh TR. Characterization of monomeric L1 metallo-beta -lactamase and the role of the N-terminal extension in negative cooperativity and antibiotic hydrolysis. J Biol Chem 2002; 277:24744-52. [PMID: 11940588 DOI: 10.1074/jbc.m201524200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The L1 metallo-beta-lactamase from Stenotrophomonas maltophilia is unique among this class of enzymes because it is tetrameric. Previous work predicted that the two regions of important intersubunit interaction were the residue Met-140 and the N-terminal extensions of each subunit. The N-terminal extension was also implicated in beta-lactam binding. Mutation of methionine 140 to aspartic acid results in a monomeric L1 beta-lactamase with a greatly altered substrate specificity profile. A 20-amino acid N-terminal deletion mutant enzyme (N-Del) could be isolated in a tetrameric form but demonstrated greatly reduced rates of beta-lactam hydrolysis and different substrate profiles compared with that of the parent enzyme. Specific site-directed mutations of individual N terminus residues were made (Y11S, W17S, and a double mutant L5A/L8A). All N-terminal mutant enzymes were tetramers and all showed higher K(m) values for ampicillin and nitrocefin, hydrolyzed ceftazidime poorly, and hydrolyzed imipenem more efficiently than ampicillin in contrast to wild-type L1. Nitrocefin turnover was significantly increased, probably because of an increased rate of breakdown of the intermediate species due to a lack of stabilizing forces. K(m) values for monomeric L1 were greatly increased for all antibiotics tested. A model of a highly mobile N-terminal extension in the monomeric enzyme is proposed to explain these findings. Tetrameric L1 shows negative cooperativity, which is not present in either the monomer or N-terminal deletion enzymes, suggesting that the cooperative effect is mediated via N-terminal intersubunit interactions. These data indicate that while the N terminus of L1 is not essential for beta-lactam hydrolysis, it is clearly important to its activity and substrate specificity.
Collapse
Affiliation(s)
- Alan M Simm
- Department of Pathology and Microbiology, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom.
| | | | | | | | | | | | | | | | | |
Collapse
|
67
|
Wehrman T, Kleaveland B, Her JH, Balint RF, Blau HM. Protein-protein interactions monitored in mammalian cells via complementation of beta -lactamase enzyme fragments. Proc Natl Acad Sci U S A 2002; 99:3469-74. [PMID: 11904411 PMCID: PMC122547 DOI: 10.1073/pnas.062043699] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
We have defined inactive alpha and omega fragments of beta-lactamase that can complement to form a functional enzyme in both bacteria and mammalian cells, serving as a readout for the interaction of proteins fused to the fragments. Critical to this advance was the identification of a tripeptide, Asn-Gly-Arg, which when juxtaposed at the carboxyl terminus of the alpha fragment increased complemented enzyme activity by up to 4 orders of magnitude. beta-Lactamase is well suited to monitoring constitutive and inducible protein interactions because it is small (29 kDa), monomeric, and assayable with a fluorescent cell-permeable substrate. The negligible background, the magnitude of induced signal caused by enzymatic amplification, and detection of signal within minutes are unparalleled in mammalian protein interaction detection systems published to date.
Collapse
Affiliation(s)
- Tom Wehrman
- Baxter Laboratory for Genetic Pharmacology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | | | | |
Collapse
|
68
|
Carenbauer AL, Garrity JD, Periyannan G, Yates RB, Crowder MW. Probing substrate binding to metallo-beta-lactamase L1 from Stenotrophomonas maltophilia by using site-directed mutagenesis. BMC BIOCHEMISTRY 2002; 3:4. [PMID: 11876827 PMCID: PMC77373 DOI: 10.1186/1471-2091-3-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2001] [Accepted: 02/13/2002] [Indexed: 11/23/2022]
Abstract
BACKGROUND The metallo-beta-lactamases are Zn(II)-containing enzymes that hydrolyze the beta-lactam bond in penicillins, cephalosporins, and carbapenems and are involved in bacterial antibiotic resistance. There are at least 20 distinct organisms that produce a metallo-beta-lactamase, and these enzymes have been extensively studied using X-ray crystallographic, computational, kinetic, and inhibition studies; however, much is still unknown about how substrates bind and the catalytic mechanism. In an effort to probe substrate binding to metallo-beta-lactamase L1 from Stenotrophomonas maltophilia, nine site-directed mutants of L1 were prepared and characterized using metal analyses, CD spectroscopy, and pre-steady state and steady state kinetics. RESULTS Site-directed mutations were generated of amino acids previously predicted to be important in substrate binding. Steady-state kinetic studies using the mutant enzymes and 9 different substrates demonstrated varying Km and kcat values for the different enzymes and substrates and that no direct correlation between Km and the effect of the mutation on substrate binding could be drawn. Stopped-flow fluorescence studies using nitrocefin as the substrate showed that only the S224D and Y228A mutants exhibited weaker nitrocefin binding. CONCLUSIONS The data presented herein indicate that Ser224, Ile164, Phe158, Tyr228, and Asn233 are not essential for tight binding of substrate to metallo-beta-lactamase L1. The results in this work also show that Km values are not reliable for showing substrate binding, and there is no correlation between substrate binding and the amount of reaction intermediate formed during the reaction. This work represents the first experimental testing of one of the computational models of the metallo-beta-lactamases.
Collapse
Affiliation(s)
- Anne L Carenbauer
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | - James D Garrity
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | - Gopal Periyannan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | - Robert B Yates
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| |
Collapse
|
69
|
Brechtel E, Huwig A, Giffhorn F. L-glucitol catabolism in Stenotrophomonas maltophilia Ac. Appl Environ Microbiol 2002; 68:582-7. [PMID: 11823194 PMCID: PMC126675 DOI: 10.1128/aem.68.2.582-587.2002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The carbohydrate catabolism of the bacterium Stenotrophomonas maltophilia Ac (previously named Pseudomonas sp. strain Ac), which is known to convert the unnatural polyol L-glucitol to D-sorbose during growth on the former as the sole source of carbon and energy, was studied in detail. All enzymes operating in a pathway that channels L-glucitol via D-sorbose into compounds of the intermediary metabolism were demonstrated, and for some prominent reactions the products of conversion were identified. D-Sorbose was converted by C-3 epimerization to D-tagatose, which, in turn, was isomerized to D-galactose. D-Galactose was the initial substrate of the De Ley-Doudoroff pathway, involving reactions of NAD-dependent oxidation of D-galactose to D-galactonate, its dehydration to 2-keto-3-deoxy-D-galactonate, and its phosphorylation to 2-keto-3-deoxy-D-galactonate 6-phosphate. Finally, aldol cleavage yielded pyruvate and D-glycerate 3-phosphate as the central metabolic intermediates.
Collapse
Affiliation(s)
- Elke Brechtel
- Lehrstuhl für Angewandte Mikrobiologie, Universität des Saarlandes, D-66041 Saarbrücken, Germany
| | | | | |
Collapse
|
70
|
Spencer J, Clarke AR, Walsh TR. Novel mechanism of hydrolysis of therapeutic beta-lactams by Stenotrophomonas maltophilia L1 metallo-beta-lactamase. J Biol Chem 2001; 276:33638-44. [PMID: 11443136 DOI: 10.1074/jbc.m105550200] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Stopped-flow tryptophan fluorescence under single turnover and pseudo-first-order conditions has been used to investigate the kinetic mechanism of beta-lactam hydrolysis by the Stenotrophomonas maltophilia L1 metallo-beta-lactamase. For the cephalosporin substrates nitrocefin and cefaclor and the carbapenem meropenem, a substantial quench of fluorescence is observed on association of substrate with enzyme. We have assigned this to a rearrangement event subsequent to formation of an initial collision complex. For the colorimetric compound nitrocefin, decay of this dark inter- mediate represents the overall rate-determining step for the reaction and is equivalent to decay of a previously observed state in which the beta-lactam amide bond has already been cleaved. For both cefaclor and meropenem, the rate-determining step for hydrolysis is loss of a second, less quenched state, in which, however, the beta-lactam amide bond remains intact. We suggest, therefore, that the mechanism of hydrolysis of nitrocefin by binuclear metallo-beta-lactamases may be atypical and that cleavage of the beta-lactam amide bond is the rate-determining step for breakdown of the majority of beta-lactam substrates by the L1 enzyme.
Collapse
Affiliation(s)
- J Spencer
- Department of Pathology and Microbiology, University of Bristol School of Medical Sciences, University Walk, Bristol BS8 1TD, United Kingdom.
| | | | | |
Collapse
|
71
|
Mercuri PS, Bouillenne F, Boschi L, Lamotte-Brasseur J, Amicosante G, Devreese B, van Beeumen J, Frère JM, Rossolini GM, Galleni M. Biochemical characterization of the FEZ-1 metallo-beta-lactamase of Legionella gormanii ATCC 33297T produced in Escherichia coli. Antimicrob Agents Chemother 2001; 45:1254-62. [PMID: 11257043 PMCID: PMC90452 DOI: 10.1128/aac.45.4.1254-1262.2001] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2000] [Accepted: 01/02/2001] [Indexed: 11/20/2022] Open
Abstract
The bla(FEZ-1) gene coding for the metallo-beta-lactamase of Legionella (Fluoribacter) gormanii ATCC 33297T was overexpressed via a T7 expression system in Escherichia coli BL21(DE3)(pLysS). The product was purified to homogeneity in two steps with a yield of 53%. The FEZ-1 metallo-beta-lactamase exhibited a broad-spectrum activity profile, with a preference for cephalosporins such as cephalothin, cefuroxime, and cefotaxime. Monobactams were not hydrolyzed. The beta-lactamase was inhibited by metal chelators. FEZ-1 is a monomeric enzyme with a molecular mass of 29,440 Da which possesses two zinc-binding sites. Its zinc content did not vary in the pH range of 5 to 9, but the presence of zinc ions modified the catalytic efficiency of the enzyme. A model of the FEZ-1 three-dimensional structure was built.
Collapse
Affiliation(s)
- P S Mercuri
- Centre d'Ingénierie des Protéines, Université de Liège, B-4000 Liège, Belgium
| | | | | | | | | | | | | | | | | | | |
Collapse
|
72
|
Abstract
The introduction of a large array of beta-lactam antibiotics has spawned the emergence of an even larger variety of beta-lactamases designed to confer resistance to these agents. beta-lactamases are produced by both gram-positive and gram-negative bacteria, but their clinical importance is far greater among the gram-negatives. The virtual explosion in our knowledge about the variety of these enzymes can often create confusion and frustration among those not well versed in the field. In this paper, we attempt to focus the discussion of beta-lactamases on those enzymes that are of the greatest clinical importance, the Ambler Class A and C enzymes. We also discuss the growing importance of the Ambler Class B metallo beta-lactamases, which hydrolyze carbapenems and are increasing in prevalence in areas of significant carbapenem usage. Copyright 2000 Harcourt Publishers Ltd.
Collapse
Affiliation(s)
- Louis B. Rice
- Medical Service, Department of Veterans Affairs Medical Center, Departments of Medicine, Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
| | | |
Collapse
|
73
|
Díaz N, Suárez D, Merz KM. Zinc Metallo-β-Lactamase from Bacteroides fragilis: A Quantum Chemical Study on Model Systems of the Active Site. J Am Chem Soc 2000. [DOI: 10.1021/ja994462s] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Natalia Díaz
- Contribution from the Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 33006, Oviedo. Spain, and 152 Davey Laboratory, Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802-6300
| | - Dimas Suárez
- Contribution from the Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 33006, Oviedo. Spain, and 152 Davey Laboratory, Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802-6300
| | - Kenneth M. Merz
- Contribution from the Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 33006, Oviedo. Spain, and 152 Davey Laboratory, Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802-6300
| |
Collapse
|
74
|
Abstract
This past year has produced determinations of X-ray crystal structures for three metallo-beta-lactamases and the elucidation of the catalytic mechanisms for a monozinc and a dizinc enzyme. These advances shed light on how such a diverse group of enzymes are evolving to inactivate so efficiently a broad spectrum of beta-lactam antibiotics.
Collapse
Affiliation(s)
- Z Wang
- The Pennsylvania State University, Department of Chemistry, 152 Davey Laboratory, University Park, PA 16802, USA
| | | | | | | |
Collapse
|