The catalytic triad of serine peptidases

Abstract.The catalytic action of serine peptidases depends on the interplay of a nucleophile, a general base and an acid. In the classic trypsin and subtilisin families this catalytic triad is composed of serine, histidine and aspartic acid residues and exhibits similar spatial arrangements, but the order of the residues in the amino acid sequence is different. By now several new families have been discovered, in which the nucleophile-base-acid pattern is generally conserved, but the individual components can vary. The variations illustrate how different groups and different protein structures achieve the same reaction.

[1]  D. Blow,et al.  Role of a Buried Acid Group in the Mechanism of Action of Chymotrypsin , 1969, Nature.

[2]  R. Henderson Structure of crystalline alpha-chymotrypsin. IV. The structure of indoleacryloyl-alpha-chyotrypsin and its relevance to the hydrolytic mechanism of the enzyme. , 1970, Journal of molecular biology.

[3]  J. Kraut 7 Chymotrypsin-Chemical Properties and Catalysis , 1971 .

[4]  R. Shulman,et al.  High resolution nuclear magnetic resonance study of the histidine--aspartate hydrogen bond in chymotrypsin and chymotrypsinogen. , 1972, Journal of molecular biology.

[5]  J. Kraut,et al.  Subtilisin; a stereochemical mechanism involving transition-state stabilization. , 1972, Biochemistry.

[6]  On the role of hydrogen-bonding system in the catalysis by serine proteases. , 1972, Acta biochimica et biophysica; Academiae Scientiarum Hungaricae.

[7]  A. Fersht,et al.  The charge relay system in chymotrypsin and chymotrypsinogen. , 1973, Journal of molecular biology.

[8]  R. Shulman,et al.  High resolution nuclear magnetic resonance studies of the active site of chymotrypsin. II. Polarization of histidine 57 by substrate analogues and competitive inhibitors. , 1974, Journal of molecular biology.

[9]  J. Kraut Serine proteases: structure and mechanism of catalysis. , 1977, Annual review of biochemistry.

[10]  D. Matthews,et al.  Re-examination of the charge relay system in subtilisin comparison with other serine proteases. , 1977, The Journal of biological chemistry.

[11]  K Worowski [Mechanism of action of proteolytic enzymes]. , 1978, Postepy higieny i medycyny doswiadczalnej.

[12]  R. Huber,et al.  Structural basis of the activation and action of trypsin , 1978 .

[13]  A. Warshel,et al.  Energetics of enzyme catalysis. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[14]  M. James An X-ray crystallographic approach to enzyme structure and function. , 1980, Canadian journal of biochemistry.

[15]  L. Polgár,et al.  Proton nuclear magnetic resonance evidence for the absence of a stable hydrogen bond between the active site aspartate and histidine residues of native subtilisins and for its presence in thiolsubtilisins. , 1981, Biochemistry.

[16]  A. Kossiakoff,et al.  Direct determination of the protonation states of aspartic acid-102 and histidine-57 in the tetrahedral intermediate of the serine proteases: neutron structure of trypsin. , 1981, Biochemistry.

[17]  L. Polgár,et al.  Current problems in mechanistic studies of serine and cysteine proteinases. , 1982, The Biochemical journal.

[18]  L. Polgár,et al.  Transition-state stabilization at the oxyanion binding sites of serine and thiol proteinases: hydrolyses of thiono and oxygen esters. , 1983, Biochemistry.

[19]  C. Kettner,et al.  Inhibition of the serine proteases leukocyte elastase, pancreatic elastase, cathepsin G, and chymotrypsin by peptide boronic acids. , 1984, The Journal of biological chemistry.

[20]  W. Bachovchin Confirmation of the assignment of the low-field proton resonance of serine proteases by using specifically nitrogen-15 labeled enzyme. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J M Ghuysen,et al.  2.8-A Structure of penicillin-sensitive D-alanyl carboxypeptidase-transpeptidase from Streptomyces R61 and complexes with beta-lactams. , 1986, The Journal of biological chemistry.

[22]  L. Polgár,et al.  Proton magnetic resonance studies of the states of ionization of histidines in native and modified subtilisins. , 1985, Biochemistry.

[23]  T. Poulos,et al.  Site-directed mutagenesis and the role of the oxyanion hole in subtilisin. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[24]  J. A. Rupley,et al.  Intramolecular cleavage of LexA and phage lambda repressors: dependence of kinetics on repressor concentration, pH, temperature, and solvent. , 1986, Biochemistry.

[25]  W. Rutter,et al.  The catalytic role of the active site aspartic acid in serine proteases. , 1987, Science.

[26]  L. Polgár Chapter 3 Structure and function of serine proteases , 1987 .

[27]  R M Stroud,et al.  The three-dimensional structure of Asn102 mutant of trypsin: role of Asp102 in serine protease catalysis. , 1988, Science.

[28]  D. Agard,et al.  Kinetic properties of the binding of alpha-lytic protease to peptide boronic acids. , 1988, Biochemistry.

[29]  J. Wells,et al.  Dissecting the catalytic triad of a serine protease , 1988, Nature.

[30]  J. W. Little,et al.  Autodigestion and RecA-dependent cleavage of Ind- mutant LexA proteins. , 1989, Journal of molecular biology.

[31]  J. Frère,et al.  Crystallographic mapping of beta-lactams bound to a D-alanyl-D-alanine peptidase target enzyme. , 1989, Journal of molecular biology.

[32]  Refined crystal structure of beta-lactamase from Citrobacter freundii indicates a mechanism for beta-lactam hydrolysis. , 1990, Nature.

[33]  L. Polgár Common feature of the four types of protease mechanism. , 1990, Biological chemistry Hoppe-Seyler.

[34]  P. Carter,et al.  Functional interaction among catalytic residues in subtilisin BPN′ , 1990, Proteins.

[35]  J. Schrag,et al.  Ser-His-Glu triad forms the catalytic site of the lipase from Geotrichum candidum , 1991, Nature.

[36]  S. N. Slilaty,et al.  The role of electrostatic interactions in the mechanism of peptide bond hydrolysis by a Ser-Lys catalytic dyad. , 1991, Protein engineering.

[37]  N. Rawlings,et al.  A new family of serine-type peptidases related to prolyl oligopeptidase. , 1991, The Biochemical journal.

[38]  D. Corey,et al.  An investigation into the minimum requirements for peptide hydrolysis by mutation of the catalytic triad of trypsin , 1992 .

[39]  Identification of potential active-site residues in the Escherichia coli leader peptidase. , 1992, The Journal of biological chemistry.

[40]  L. Polgár Structural relationship between lipases and peptidases of the prolyl oligopeptidase family , 1992, FEBS letters.

[41]  C. Betzel,et al.  Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution , 1992, Nature.

[42]  B. Dunn,et al.  Substrate specificity and kinetic properties of pepstatin-insensitive carboxyl proteinase from Pseudomonas sp. No. 101. , 1992, Biochimica et biophysica acta.

[43]  P. G. Gassman,et al.  Understanding the rates of certain enzyme-catalyzed reactions: proton abstraction from carbon acids, acyl-transfer reactions, and displacement reactions of phosphodiesters. , 1993, Biochemistry.

[44]  M. Jaskólski,et al.  Crystal structure of Escherichia coli L-asparaginase, an enzyme used in cancer therapy. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[45]  R. Dalbey,et al.  A serine and a lysine residue implicated in the catalytic mechanism of the Escherichia coli leader peptidase. , 1993, The Journal of biological chemistry.

[46]  J. L. Smith,et al.  Structure of the allosteric regulatory enzyme of purine biosynthesis. , 1994, Science.

[47]  Marc Allaire,et al.  Picornaviral 3C cysteine proteinases have a fold similar to chymotrypsin-like serine proteinases , 1994, Nature.

[48]  P. Frey,et al.  A low-barrier hydrogen bond in the catalytic triad of serine proteases. , 1994, Science.

[49]  C. Betzel,et al.  Crystallographic studies of Savinase, a subtilisin-like proteinase, at pH 10.5. , 1994, European journal of biochemistry.

[50]  Low‐Barrier Hydrogen Bonds and Enzymic Catalysis. , 1994 .

[51]  C. Craik,et al.  Structural basis of substrate specificity in the serine proteases , 1995, Protein science : a publication of the Protein Society.

[52]  A. Kuzin,et al.  The refined crystallographic structure of a DD-peptidase penicillin-target enzyme at 1.6 A resolution. , 1995, Journal of molecular biology.

[53]  Janet L. Schottel,et al.  A novel variant of the catalytic triad in the Streptomyces scabies esterase , 1995, Nature Structural Biology.

[54]  P A Kollman,et al.  On low-barrier hydrogen bonds and enzyme catalysis. , 1995, Science.

[55]  R. Huber,et al.  Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution. , 1995, Science.

[56]  Eleanor J. Dodson,et al.  Penicillin acylase has a single-amino-acid catalytic centre , 1996, Nature.

[57]  J. Guthrie Short strong hydrogen bonds: can they explain enzymic catalysis? , 1996, Chemistry & biology.

[58]  A. Wlodawer,et al.  A covalently bound catalytic intermediate in Escherichia coli asparaginase : Crystal structure of a Thr‐89‐Val mutant , 1996, FEBS letters.

[59]  C. J. Murray,et al.  A low-barrier hydrogen bond in subtilisin: 1H and 15N NMR studies with peptidyl trifluoromethyl ketones. , 1996, Biochemistry.

[60]  David A. Matthews,et al.  Structure of the Human Cytomegalovirus Protease Catalytic Domain Reveals a Novel Serine Protease Fold and Catalytic Triad , 1996, Cell.

[61]  J. Culp,et al.  Unique fold and active site in cytomegalovirus protease , 1996, Nature.

[62]  E. G. Frank,et al.  Structure of the UmuD′ protein and its regulation in response to DNA damage , 1996, Nature.

[63]  P. Kloetzel,et al.  Analysis of mammalian 20S proteasome biogenesis: the maturation of beta‐subunits is an ordered two‐step mechanism involving autocatalysis. , 1996, The EMBO journal.

[64]  J. Frère,et al.  The catalytic mechanism of beta-lactamases: NMR titration of an active-site lysine residue of the TEM-1 enzyme. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[65]  P. Bonneau,et al.  A new serine-protease fold revealed by the crystal structure of human cytomegalovirus protease , 1996, Nature.

[66]  M. Hochstrasser,et al.  Autocatalytic Subunit Processing Couples Active Site Formation in the 20S Proteasome to Completion of Assembly , 1996, Cell.

[67]  R. Kurumbail,et al.  Three-dimensional structure of human cytomegalovirus protease , 1996, Nature.

[68]  M. Orłowski,et al.  Reactions of [14C]-3,4-dichloroisocoumarin with subunits of pituitary and spleen multicatalytic proteinase complexes (proteasomes). , 1997, Biochemistry.

[69]  P. Frey,et al.  Understanding enzymic catalysis: the importance of short, strong hydrogen bonds. , 1997, Chemistry & biology.

[70]  J. Culp,et al.  Crystal structure of varicella-zoster virus protease. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[71]  A. Goldberg,et al.  Covalent modification of the active site threonine of proteasomal beta subunits and the Escherichia coli homolog HslV by a new class of inhibitors. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[72]  P. Frey,et al.  A new concept for the mechanism of action of chymotrypsin: the role of the low-barrier hydrogen bond. , 1997, Biochemistry.

[73]  E. D. De Fabo,et al.  A low-barrier hydrogen bond in the catalytic triad of serine proteases? Theory versus experiment. , 1997, Science.

[74]  M. James,et al.  The refined crystal structure of the 3C gene product from hepatitis A virus: specific proteinase activity and RNA recognition , 1997, Journal of virology.

[75]  M. Paetzel,et al.  Catalytic hydroxyl/amine dyads within serine proteases. , 1997, Trends in biochemical sciences.

[76]  N. Road Refined X-ray Crystallographic Structure of the Poliovirus 3C Gene Product , 1997 .

[77]  R. Huber,et al.  Structure of 20S proteasome from yeast at 2.4Å resolution , 1997, Nature.

[78]  S. Bron,et al.  The chemistry and enzymology of the type I signal peptidases , 1997, Protein science : a publication of the Protein Society.

[79]  R. Huber,et al.  Conformational constraints for protein self-cleavage in the proteasome. , 1998, Journal of molecular biology.

[80]  László Polgár,et al.  Prolyl Oligopeptidase An Unusual β-Propeller Domain Regulates Proteolysis , 1998, Cell.

[81]  Robert Huber,et al.  Contribution of Proteasomal β-Subunits to the Cleavage of Peptide Substrates Analyzed with Yeast Mutants* , 1998, The Journal of Biological Chemistry.

[82]  A Wlodawer,et al.  Catalytic triads and their relatives. , 1998, Trends in biochemical sciences.

[83]  P A Frey,et al.  The Low Barrier Hydrogen Bond in Enzymatic Catalysis* , 1998, The Journal of Biological Chemistry.

[84]  P. Kuhn,et al.  The 0.78 A structure of a serine protease: Bacillus lentus subtilisin. , 1998, Biochemistry.

[85]  V. Fülöp,et al.  Prolyl oligopeptidase: an unusual beta-propeller domain regulates proteolysis. , 1998, Cell.

[86]  S. Abdel-Meguid,et al.  Site-directed mutagenesis probing the catalytic role of arginines 165 and 166 of human cytomegalovirus protease. , 1998, Biochemistry.

[87]  P. Frey,et al.  Fractionation factors and activation energies for exchange of the low barrier hydrogen bonding proton in peptidyl trifluoromethyl ketone complexes of chymotrypsin. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[88]  N. Rawlings,et al.  Tripeptidyl-peptidase I is apparently the CLN2 protein absent in classical late-infantile neuronal ceroid lipofuscinosis. , 1999, Biochimica et biophysica acta.

[89]  W. Baumeister,et al.  The 26S proteasome: a molecular machine designed for controlled proteolysis. , 1999, Annual review of biochemistry.

[90]  J. Otlewski,et al.  Structural and energetic determinants of the S1-site specificity in serine proteases. , 1999, European journal of biochemistry.

[91]  M. Paetzel,et al.  Common protein architecture and binding sites in proteases utilizing a Ser/Lys dyad mechanism , 2008, Protein science : a publication of the Protein Society.

[92]  S. Abdel-Meguid,et al.  Human Herpesvirus Proteases , 1999 .

[93]  P. Darke,et al.  The Herpesvirus Proteases as Targets for Antiviral Chemotherapy , 2000, Antiviral chemistry & chemotherapy.

[94]  P. Frey,et al.  The deuterium isotope effect on the NMR signal of the low-barrier hydrogen bond in a transition-state analog complex of chymotrypsin. , 2000, Biochemical and biophysical research communications.

[95]  L. Polgár,et al.  Substrate‐ and pH‐dependent contribution of oxyanion binding site to the catalysis of prolyl oligopeptidase, a paradigm of the serine oligopeptidase family , 2008, Protein science : a publication of the Protein Society.

[96]  M. Lewis,et al.  Crystal structure of the lambda repressor C-terminal domain provides a model for cooperative operator binding. , 2000, Cell.

[97]  M. Lewis,et al.  Crystal Structure of the λ Repressor C-Terminal Domain Provides a Model for Cooperative Operator Binding , 2000, Cell.

[98]  P. Lobel,et al.  The Human CLN2 Protein/Tripeptidyl-Peptidase I Is a Serine Protease That Autoactivates at Acidic pH* , 2001, The Journal of Biological Chemistry.

[99]  A. Wlodawer,et al.  Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase. , 2001, Biochemistry.

[100]  F. Winkler,et al.  Refined crystal structure of beta-lactamase from Citrobacter freundii indicates a mechanism for beta-lactam hydrolysis. , 2001, Nature.

[101]  L. Tong,et al.  Molecular mechanism for dimerization to regulate the catalytic activity of human cytomegalovirus protease , 2001, Nature Structural Biology.

[102]  A. Wlodawer,et al.  Do bacterial L-asparaginases utilize a catalytic triad Thr-Tyr-Glu? , 2001, Biochimica et biophysica acta.

[103]  Thiolate-imidazolium ion pair is not an obligatory catalytic entity of cysteine peptidases: the active site of picornain 3C. , 2001, Biochemistry.

[104]  Kohei Oda,et al.  Carboxyl proteinase from Pseudomonas defines a novel family of subtilisin-like enzymes , 2001, Nature Structural Biology.

[105]  Structural Studies of Herpesvirus Proteases , 2001 .

[106]  Richard A. Pfuetzner,et al.  Crystal Structure of LexA A Conformational Switch for Regulation of Self-Cleavage , 2001, Cell.

[107]  A Wlodawer,et al.  Structural basis for the activity and substrate specificity of Erwinia chrysanthemi L-asparaginase. , 2001, Biochemistry.

[108]  L. Tong,et al.  Investigating the role of histidine 157 in the catalytic activity of human cytomegalovirus protease. , 2001, Biochemistry.

[109]  L. Hedstrom Serine protease mechanism and specificity. , 2002, Chemical reviews.

[110]  V. Fülöp,et al.  Substrate-dependent Competency of the Catalytic Triad of Prolyl Oligopeptidase* , 2002, The Journal of Biological Chemistry.

[111]  Neil D. Rawlings,et al.  MEROPS: the protease database , 2002, Nucleic Acids Res..

[112]  A. Wlodawer,et al.  Atomic resolution structure of Erwinia chrysanthemi L-asparaginase. , 2002, Acta crystallographica. Section D, Biological crystallography.

[113]  N. Silvaggi,et al.  The crystal structure of phosphonate-inhibited D-Ala-D-Ala peptidase reveals an analogue of a tetrahedral transition state. , 2003, Biochemistry.

[114]  L. Polgár,et al.  The unusual catalytic triad of poliovirus protease 3C. , 2003, Biochemistry.

[115]  Kohei Oda,et al.  Structural and enzymatic properties of the sedolisin family of serine-carboxyl peptidases. , 2003, Acta biochimica Polonica.

[116]  A. Wlodawer,et al.  A model of tripeptidyl-peptidase I (CLN2), a ubiquitous and highly conserved member of the sedolisin family of serine-carboxyl peptidases , 2003, BMC Structural Biology.

[117]  Toru Nakayama,et al.  Crystallographic and Biochemical Investigations of Kumamolisin-As, a Serine-Carboxyl Peptidase with Collagenase Activity* , 2004, Journal of Biological Chemistry.

[118]  P. Ortiz de Montellano,et al.  Communication between the active sites and dimer interface of a herpesvirus protease revealed by a transition-state inhibitor. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[119]  W. Dalton,et al.  The proteasome. , 2004, Seminars in oncology.

[120]  A. Wlodawer,et al.  Classification of ATP-dependent proteases Lon and comparison of the active sites of their proteolytic domains. , 2004, European journal of biochemistry.

[121]  A. Wlodawer,et al.  The Catalytic Domain of Escherichia coli Lon Protease Has a Unique Fold and a Ser-Lys Dyad in the Active Site* , 2004, Journal of Biological Chemistry.

[122]  V. Dembitsky,et al.  Recent advances in the medicinal chemistry of alpha-aminoboronic acids, amine-carboxyboranes and their derivatives. , 2004, Mini reviews in medicinal chemistry.

[123]  R. Huber,et al.  Inhibitors of the eukaryotic 20S proteasome core particle: a structural approach. , 2004, Biochimica et biophysica acta.