Three-dimensional structure of the quorum-quenching N-acyl homoserine lactone hydrolase from Bacillus thuringiensis.

The three-dimensional structure of the N-acyl-l-homoserine lactone hydrolase (AHL lactonase) from Bacillus thuringiensis has been determined, by using single-wavelength anomalous dispersion (SAD) phasing, to 1.6-angstroms resolution. AHLs are produced by many Gram-negative bacteria as signaling molecules used in quorum-sensing pathways that indirectly sense cell density and regulate communal behavior. Because of their importance in pathogenicity, quorum-sensing pathways have been suggested as potential targets for the development of novel therapeutics. Quorum-sensing can be disrupted by enzymes evolved to degrade these lactones, such as AHL lactonases. These enzymes are members of the metallo-beta-lactamase superfamily and contain two zinc ions in their active sites. The zinc ions are coordinated to a number of ligands, including a single oxygen of a bridging carboxylate and a bridging water/hydroxide ion, thought to be the nucleophile that hydrolyzes the AHLs to ring-opened products, which can no longer act as quorum signals.

[1]  Thomas C. Terwilliger,et al.  Electronic Reprint Biological Crystallography Maximum-likelihood Density Modification , 2022 .

[2]  Marc S. Lewis,et al.  Modern analytical ultracentrifugation in protein science: A tutorial review , 2002, Protein science : a publication of the Protein Society.

[3]  K. V. van Holde,et al.  Boundary analysis of sedimentation‐velocity experiments with monodisperse and paucidisperse solutes , 1978 .

[4]  T. Wood,et al.  Inhibition of biofilm formation and swarming of Escherichia coli by (5Z)-4-bromo-5-(bromomethylene)-3-butyl-2(5H)-furanone. , 2001, Environmental microbiology.

[5]  N. A. Whitehead,et al.  The regulation of virulence in phytopathogenic Erwinia species: quorum sensing, antibiotics and ecological considerations , 2002, Antonie van Leeuwenhoek.

[6]  M. G. Rossmann,et al.  International Tables for Crystallography: Crystallography of biological macromolecules , 2006 .

[7]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[8]  M. Crowder,et al.  Mutational Analysis of Metallo-β-lactamase CcrA from Bacteroides fragilis† , 2000 .

[9]  D. S. Moss,et al.  TLSANL: TLS parameter-analysis program for segmented anisotropic refinement of macromolecular structures , 1993 .

[10]  S J Wodak,et al.  SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. , 1999, Acta crystallographica. Section D, Biological crystallography.

[11]  A. Carenbauer,et al.  Metal Binding Asp-120 in Metallo-β-lactamase L1 from Stenotrophomonas maltophilia Plays a Crucial Role in Catalysis* , 2004, Journal of Biological Chemistry.

[12]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[13]  A D Cameron,et al.  Crystal structure of human glyoxalase II and its complex with a glutathione thiolester substrate analogue. , 1999, Structure.

[14]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[15]  J. Frère,et al.  The 3‐D structure of a zinc metallo‐beta‐lactamase from Bacillus cereus reveals a new type of protein fold. , 1995 .

[16]  Ricardo Martí-Arbona,et al.  Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli. , 2005, Biochemistry.

[17]  D. Christianson,et al.  Structural biology of zinc. , 1991, Advances in protein chemistry.

[18]  Eddy Arnold,et al.  Crystallography of biological macromolecules , 2001 .

[19]  O. Pellegrini,et al.  Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z , 2005, Nature.

[20]  Thomas C. Terwilliger,et al.  Automated MAD and MIR structure solution , 1999, Acta crystallographica. Section D, Biological crystallography.

[21]  Chris Sander,et al.  Touring protein fold space with Dali/FSSP , 1998, Nucleic Acids Res..

[22]  Lian-Hui Zhang,et al.  AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora , 2000 .

[23]  S. Lewenza,et al.  Interspecies communication between Burkholderia cepacia and Pseudomonas aeruginosa. , 2002, Canadian journal of microbiology.

[24]  Say Leong Ong,et al.  Acyl‐homoserine lactone acylase from Ralstonia strain XJ12B represents a novel and potent class of quorum‐quenching enzymes , 2003, Molecular microbiology.

[25]  P. Kraulis A program to produce both detailed and schematic plots of protein structures , 1991 .

[26]  G. Petsko,et al.  Inhibition of the aminopeptidase from Aeromonas proteolytica by L-leucinephosphonic acid. Spectroscopic and crystallographic characterization of the transition state of peptide hydrolysis. , 2001, Biochemistry.

[27]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[28]  E. Greenberg,et al.  Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing. , 2001, Annual review of genetics.

[29]  I. Taylor,et al.  The crystal structure of the L1 metallo-beta-lactamase from Stenotrophomonas maltophilia at 1.7 A resolution. , 1998, Journal of molecular biology.

[30]  E. Lattman,et al.  Representation of phase probability distributions for simplified combination of independent phase information , 1970 .

[31]  Dagmar Ringe,et al.  POVScript+: a program for model and data visualization using persistence of vision ray-tracing , 2003 .

[32]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[33]  Hiromi Daiyasu,et al.  Expansion of the zinc metallo‐hydrolase family of the β‐lactamase fold , 2001 .

[34]  D. McRee,et al.  A visual protein crystallographic software system for X11/Xview , 1992 .

[35]  Lian-Hui Zhang,et al.  Quorum sensing and quorum-quenching enzymes. , 2005, Journal of microbiology.

[36]  E A Merritt,et al.  Expanding the model: anisotropic displacement parameters in protein structure refinement. , 1999, Acta crystallographica. Section D, Biological crystallography.

[37]  J. Frère,et al.  Biochemical Characterization of the FEZ-1 Metallo-β-Lactamase of Legionella gormanii ATCC 33297T Produced in Escherichia coli , 2001, Antimicrobial Agents and Chemotherapy.

[38]  Lian-Hui Zhang,et al.  Specificity and Enzyme Kinetics of the Quorum-quenching N-Acyl Homoserine Lactone Lactonase (AHL-lactonase)* , 2004, Journal of Biological Chemistry.

[39]  Kristina M Smith,et al.  Molecular mechanisms of bacterial quorum sensing as a new drug target. , 2003, Current opinion in chemical biology.

[40]  B. Matthews,et al.  Escherichia coli methionine aminopeptidase: implications of crystallographic analyses of the native, mutant, and inhibited enzymes for the mechanism of catalysis. , 1999, Biochemistry.

[41]  Stephen J. Benkovic,et al.  Metallo-β-lactamase: structure and mechanism , 1999 .

[42]  G N Murshudov,et al.  Use of TLS parameters to model anisotropic displacements in macromolecular refinement. , 2001, Acta crystallographica. Section D, Biological crystallography.

[43]  D. Ringe,et al.  Proteins in organic solvents. , 2001, Current opinion in structural biology.

[44]  Walter Fast,et al.  The quorum-quenching lactonase from Bacillus thuringiensis is a metalloprotein. , 2005, Biochemistry.

[45]  E. Greenberg,et al.  Sociomicrobiology: the connections between quorum sensing and biofilms. , 2005, Trends in microbiology.

[46]  Miguel Teixeira,et al.  Structure of a dioxygen reduction enzyme from Desulfovibrio gigas , 2000, Nature Structural Biology.

[47]  J. Richardson,et al.  The anatomy and taxonomy of protein structure. , 1981, Advances in protein chemistry.

[48]  G. Barton,et al.  Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels , 1992, Proteins.

[49]  R. Ulrich,et al.  Quorum Sensing: a Transcriptional Regulatory System Involved in the Pathogenicity of Burkholderia mallei , 2004, Infection and Immunity.

[50]  P. Fitzgerald,et al.  Unanticipated inhibition of the metallo-beta-lactamase from Bacteroides fragilis by 4-morpholineethanesulfonic acid (MES): a crystallographic study at 1.85-A resolution. , 1998, Biochemistry.

[51]  A. Marchfelder,et al.  Zinc- and iron-dependent cytosolic metallo-beta-lactamase domain proteins exhibit similar zinc-binding affinities, independent of an atypical glutamate at the metal-binding site. , 2005, The Biochemical journal.