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Binding of hydroxamic acid inhibitors to crystalline thermolysin suggests a pentacoordinate zinc intermediate in catalysis.

Holmes MA, Matthews BW
Biochemistry 20 6912-20 (1981)
Cited: 99 times
EuropePMC logo PMID: 7317361

Reviews - 4tln mentioned but not cited (1)

  1. Overview of protein structural and functional folds. Sun PD, Foster CE, Boyington JC. Curr Protoc Protein Sci Chapter 17 Unit 17.1 (2004)

Articles - 4tln mentioned but not cited (10)

  1. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. Huang B, Schroeder M. BMC Struct Biol 6 19 (2006)
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  3. Assessment of programs for ligand binding affinity prediction. Kim R, Skolnick J. J Comput Chem 29 1316-1331 (2008)
  4. Development of quantitative structure-binding affinity relationship models based on novel geometrical chemical descriptors of the protein-ligand interfaces. Zhang S, Golbraikh A, Tropsha A. J Med Chem 49 2713-2724 (2006)
  5. Acoustic methods for high-throughput protein crystal mounting at next-generation macromolecular crystallographic beamlines. Roessler CG, Kuczewski A, Stearns R, Ellson R, Olechno J, Orville AM, Allaire M, Soares AS, Héroux A. J Synchrotron Radiat 20 805-808 (2013)
  6. A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral membrane metallopeptidases. López-Pelegrín M, Cerdà-Costa N, Martínez-Jiménez F, Cintas-Pedrola A, Canals A, Peinado JR, Marti-Renom MA, López-Otín C, Arolas JL, Gomis-Rüth FX. J Biol Chem 288 21279-21294 (2013)
  7. Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes. Yin X, Scalia A, Leroy L, Cuttitta CM, Polizzo GM, Ericson DL, Roessler CG, Campos O, Ma MY, Agarwal R, Jackimowicz R, Allaire M, Orville AM, Sweet RM, Soares AS. Acta Crystallogr D Biol Crystallogr 70 1177-1189 (2014)
  8. Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening. Cuttitta CM, Ericson DL, Scalia A, Roessler CG, Teplitsky E, Joshi K, Campos O, Agarwal R, Allaire M, Orville AM, Sweet RM, Soares AS. Acta Crystallogr D Biol Crystallogr 71 94-103 (2015)
  9. Using sound pulses to solve the crystal-harvesting bottleneck. Samara YN, Brennan HM, McCarthy L, Bollard MT, Laspina D, Wlodek JM, Campos SL, Natarajan R, Gofron K, McSweeney S, Soares AS, Leroy L. Acta Crystallogr D Struct Biol 74 986-999 (2018)
  10. MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature. Shivashankar N, Patil S, Bhosle A, Chandra N, Natarajan V. BMC Bioinformatics 17 26 (2016)


Reviews citing this publication (8)

  1. Molecular and biotechnological aspects of microbial proteases. Rao MB, Tanksale AM, Ghatge MS, Deshpande VV. Microbiol Mol Biol Rev 62 597-635 (1998)
  2. Structure, mechanism, and inhibition of histone deacetylases and related metalloenzymes. Lombardi PM, Cole KE, Dowling DP, Christianson DW. Curr Opin Struct Biol 21 735-743 (2011)
  3. The thermolysin family (M4) of enzymes: therapeutic and biotechnological potential. Adekoya OA, Sylte I. Chem Biol Drug Des 73 7-16 (2009)
  4. The esterases: perspectives and problems. Aldridge WN. Chem Biol Interact 87 5-13 (1993)
  5. Mammalian metalloendopeptidases. Bond JS, Beynon RJ. Int J Biochem 17 565-574 (1985)
  6. Design and use of potent, specific enzyme inhibitors. Stark GR, Bartlett PA. Pharmacol Ther 23 45-78 (1983)
  7. Determinants of molecular reactivity as criteria for predicting toxicity: problems and approaches. Weinstein H, Rabinowitz J, Liebman MN, Osman R. Environ Health Perspect 61 147-162 (1985)
  8. The Structures and Binding Modes of Small-Molecule Inhibitors of Pseudomonas aeruginosa Elastase LasB. Camberlein V, Jézéquel G, Haupenthal J, Hirsch AKH. Antibiotics (Basel) 11 1060 (2022)

Articles citing this publication (80)

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  3. Structure of thermolysin refined at 1.6 A resolution. Holmes MA, Matthews BW. J Mol Biol 160 623-639 (1982)
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  6. The structural basis for substrate and inhibitor selectivity of the anthrax lethal factor. Turk BE, Wong TY, Schwarzenbacher R, Jarrell ET, Leppla SH, Collier RJ, Liddington RC, Cantley LC. Nat Struct Mol Biol 11 60-66 (2004)
  7. Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution. Volbeda A, Lahm A, Sakiyama F, Suck D. EMBO J 10 1607-1618 (1991)
  8. A slow, tight-binding inhibitor of the zinc-dependent deacetylase LpxC of lipid A biosynthesis with antibiotic activity comparable to ciprofloxacin. McClerren AL, Endsley S, Bowman JL, Andersen NH, Guan Z, Rudolph J, Raetz CR. Biochemistry 44 16574-16583 (2005)
  9. Antibacterial activities and characterization of novel inhibitors of LpxC. Clements JM, Coignard F, Johnson I, Chandler S, Palan S, Waller A, Wijkmans J, Hunter MG. Antimicrob Agents Chemother 46 1793-1799 (2002)
  10. Antibacterial agents that target lipid A biosynthesis in gram-negative bacteria. Inhibition of diverse UDP-3-O-(r-3-hydroxymyristoyl)-n-acetylglucosamine deacetylases by substrate analogs containing zinc binding motifs. Jackman JE, Fierke CA, Tumey LN, Pirrung M, Uchiyama T, Tahir SH, Hindsgaul O, Raetz CR. J Biol Chem 275 11002-11009 (2000)
  11. X-ray structures of human neutrophil collagenase complexed with peptide hydroxamate and peptide thiol inhibitors. Implications for substrate binding and rational drug design. Grams F, Reinemer P, Powers JC, Kleine T, Pieper M, Tschesche H, Huber R, Bode W. Eur J Biochem 228 830-841 (1995)
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  17. Isolation of cDNAs for LCE and HCE, two constituent proteases of the hatching enzyme of Oryzias latipes, and concurrent expression of their mRNAs during development. Yasumasu S, Yamada K, Akasaka K, Mitsunaga K, Iuchi I, Shimada H, Yamagami K. Dev Biol 153 250-258 (1992)
  18. Characterization and crystal structure of zinc azurin, a by-product of heterologous expression in Escherichia coli of Pseudomonas aeruginosa copper azurin. Nar H, Huber R, Messerschmidt A, Filippou AC, Barth M, Jaquinod M, van de Kamp M, Canters GW. Eur J Biochem 205 1123-1129 (1992)
  19. Unusual zinc-binding mode of HDAC6-selective hydroxamate inhibitors. Porter NJ, Mahendran A, Breslow R, Christianson DW. Proc Natl Acad Sci U S A 114 13459-13464 (2017)
  20. The structure of the Aeromonas proteolytica aminopeptidase complexed with a hydroxamate inhibitor. Involvement in catalysis of Glu151 and two zinc ions of the co-catalytic unit. Chevrier B, D'Orchymont H, Schalk C, Tarnus C, Moras D. Eur J Biochem 237 393-398 (1996)
  21. Synergistic anti-human immunodeficiency virus type 1 effect of hydroxamate compounds with 2',3'-dideoxyinosine in infected resting human lymphocytes. Malley SD, Grange JM, Hamedi-Sangsari F, Vila JR. Proc Natl Acad Sci U S A 91 11017-11021 (1994)
  22. Structure and stability of thermophilic enzymes. Studies on thermolysin. Fontana A. Biophys Chem 29 181-193 (1988)
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  32. Differences in the structural requirements for selective interaction with neutral metalloendopeptidase (enkephalinase) or angiotensin-converting enzyme. Molecular investigation by use of new thiol inhibitors. Fournie-Zaluski MC, Lucas E, Waksman G, Roques BP. Eur J Biochem 139 267-274 (1984)
  33. Structure of prokaryotic polyamine deacetylase reveals evolutionary functional relationships with eukaryotic histone deacetylases. Lombardi PM, Angell HD, Whittington DA, Flynn EF, Rajashankar KR, Christianson DW. Biochemistry 50 1808-1817 (2011)
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  37. Entropy as a Driver of Selectivity for Inhibitor Binding to Histone Deacetylase 6. Porter NJ, Wagner FF, Christianson DW. Biochemistry 57 3916-3924 (2018)
  38. Inhibition of metalloproteinases in Bothrops asper venom by endogenous peptides. Francis B, Kaiser II. Toxicon 31 889-899 (1993)
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  43. Amino hydroxamic acids as potent inhibitors of leukotriene A4 hydrolase. Hogg JH, Ollmann IR, Haeggström JZ, Wetterholm A, Samuelsson B, Wong CH. Bioorg Med Chem 3 1405-1415 (1995)
  44. A shape- and chemistry-based docking method and its use in the design of HIV-1 protease inhibitors. DesJarlais RL, Dixon JS. J Comput Aided Mol Des 8 231-242 (1994)
  45. Inhibition of arginine gingipains (RgpB and HRgpA) with benzamidine inhibitors: zinc increases inhibitory potency. Krauser JA, Potempa J, Travis J, Powers JC. Biol Chem 383 1193-1198 (2002)
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Related citations provided by authors (14)

  1. Structure of Thermolysin Refined at 1.6 Angstroms Resolution. Holmes MA, Matthews BW J. Mol. Biol. 160 623- (1982)
  2. Structure of a Mercaptan-Thermolysin Complex Illustrates Mode of Inhibition of Zinc Proteases by Substrate-Analogue Mercaptans. Monzingo AF, Matthews BW Biochemistry 21 3390- (1982)
  3. Binding of the Biproduct Analog L-Benzylsuccinic Acid to Thermolysin Determined by X-Ray Crystallography. Bolognesi MC, Matthews BW J. Biol. Chem. 254 634- (1979)
  4. Comparison of the Structures of Carboxypeptidase a and Thermolysin. Kester WR, Matthews BW J. Biol. Chem. 252 7704- (1977)
  5. A Crystallographic Study of the Complex of Phosphoramidon with Thermolysin. A Model for the Presumed Catalytic Transition State and for the Binding of Extended Substrates. Weaver LH, Kester WR, Matthews BW J. Mol. Biol. 114 119- (1977)
  6. Crystallographic Study of the Binding of Dipeptide Inhibitors to Thermolysin. Implications for the Mechanism of Catalysis. Kester WR, Matthews BW Biochemistry 16 2506- (1977)
  7. Role of Calcium in the Thermal Stability of Thermolysin. Dahlquist FW, Long JW, Bigbee WL Biochemistry 15 1103- (1976)
  8. Evidence of Homologous Relationship between Thermolysin and Neutral Protease a of Bacillus Subtilis. Levy PL, Pangburn MK, Burstein Y, Ericsson LH, Neurath H, Walsh KA Proc. Natl. Acad. Sci. U.S.A. 72 4341- (1975)
  9. The Conformation of Thermolysin. Matthews BW, Weaver LH, Kester WR J. Biol. Chem. 249 8030- (1974)
  10. Binding of Lanthanide Ions to Thermolysin. Matthews BW, Weaver LH Biochemistry 13 1719- (1974)
  11. The Structure of Thermolysin,an Electron Density Map at 2.3 Angstroms Resolution. Colman PM, Jansonius JN, Matthews BW J. Mol. Biol. 70 701- (1972)
  12. Amino-Acid Sequence of Thermolysin. Titani K, Hermodson MA, Ericsson LH, Walsh KA, Neurath H Nature New Biol. 238 35- (1972)
  13. Three Dimensional Structure of Thermolysin. Matthews BW, Jansonius JN, Colman PM, Schoenborn BP, Duporque D Nature New Biol. 238 37- (1972)
  14. Structure of Thermolysin. Matthews BW, Colman PM, Jansonius JN, Titani K, Walsh KA, Neurath H Nature New Biol. 238 41- (1972)

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