Evolutionary families of peptidase inhibitors

Rawlings, Neil D.; Tolle, Dominic P.; Barrett, Alan J.

doi:10.1042/bj20031825

Cited by 552 publications

(450 citation statements)

References 105 publications

Supporting

Mentioning

414

Contrasting

Unclassified

Order By: Relevance

“…Rawlings et al (25) have identified 13 clans of Laskowski serine protease inhibitors with distinct 3D folds, indicating that the mechanism has evolved many times. At present, however, there are very few examples of inhibition of other protease types by a mechanism in which a peptide segment binds in a substrate-like manner and resists hydrolysis (25). The best-characterized example appears to be Streptomyces metalloproteinase inhibitor (SMPI) (46), but this inhibitor is much more susceptible to hydrolysis than most of the serine protease inhibitors, with a turnover time of Ͻ10 min when bound to thermolysin (46).…”

Section: B Amentioning

confidence: 99%

“…Since then, it has been found that SBTI is one of a very large number of inhibitors, described as ''standard mechanism'' or ''Laskowski mechanism'' inhibitors, that act by binding tightly to the active sites of their targets as a substrate would, but resist hydrolysis for many hours or longer (22)(23)(24)(25). Because the products of hydrolysis remain physically associated, the resynthesis of these inhibitors is an intramolecular reaction and is, therefore, much more favorable than the equivalent intermolecular reaction at modest reactant concentrations.…”

mentioning

confidence: 99%

“…Because the products of hydrolysis remain physically associated, the resynthesis of these inhibitors is an intramolecular reaction and is, therefore, much more favorable than the equivalent intermolecular reaction at modest reactant concentrations. Despite the prevalence of Laskowski inhibitors (25), the mechanisms by which they resist proteolysis remain poorly understood (26)(27)(28)(29).…”

mentioning

confidence: 99%

See 2 more Smart Citations

Structure of a serine protease poised to resynthesize a peptide bond

Zakharova

Horvath

Goldenberg

2009

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The serine proteases are among the most thoroughly studied enzymes, and numerous crystal structures representing the enzymesubstrate complex and intermediates in the hydrolysis reactions have been reported. Some aspects of the catalytic mechanism remain controversial, however, especially the role of conformational changes in the reaction. We describe here a high-resolution (1.46 Å) crystal structure of a complex formed between a cleaved form of bovine pancreatic trypsin inhibitor (BPTI) and a catalytically inactive trypsin variant with the BPTI cleavage site ideally positioned in the active site for resynthesis of the peptide bond. This structure defines the positions of the newly generated amino and carboxyl groups following the 2 steps in the hydrolytic reaction. Comparison of this structure with those representing other intermediates in the reaction demonstrates that the residues of the catalytic triad are positioned to promote each step of both the forward and reverse reaction with remarkably little motion and with conservation of hydrogen-bonding interactions. The results also provide insights into the mechanism by which inhibitors like BPTI normally resist hydrolysis when bound to their target proteases.trypsin ͉ bovine pancreatic trypsin inhibitor ͉ enzyme mechanisms S erine proteases are found throughout all 3 domains of cellular life and function in a wide range of physiological processes, including digestion, protein maturation and turnover, hemostasis, and immune responses (1). Approximately 0.6% of human protein-encoding genes are predicted to specify serine proteases, and this family is even more prevalent in other organisms, notably the arthropods (2, 3). A large body of biochemical and structural data have established a 2-step mechanism for hydrolysis of peptide bonds by this class of proteases (4), as shown in Scheme 1.The first step of the reaction is a nucleophilic attack by the catalytic serine residue (Ser-195 in trypsin and other members of the chymotrypsin, or S1, family) on the carbonyl carbon atom of the residue labeled P1, generating a covalent acyl-enzyme intermediate and a new peptide amino terminus, on the P1Ј residue. A second nucleophilic attack, by a water molecule, leads to hydrolysis of the acyl-enzyme, releasing the new carboxyl group and restoring the catalytic Ser residue to its initial state.

show abstract

Section: B Amentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Structure of a serine protease poised to resynthesize a peptide bond

Zakharova

Horvath

Goldenberg

2009

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…The presence of a leucine (leucyl) aminopeptidase (LAP) and a (LAP)-related protein in the genome and secretome is an important finding. LAPs are often viewed as cell maintenance enzymes with critical roles in turnover of peptides (Rawlings et al, 2004). Some LAPs may bind DNA enabling them to serve as transcriptional repressors that control pyrimidine, alginate and cholera toxin biosynthesis, as well as mediate sitespecific recombination events in plasmids and phages (Matsui et al, 2006).…”

Section: Vibrio Coralliilyticus Genome E De O Santos Et Almentioning

confidence: 99%

Genomic and proteomic analyses of the coral pathogen Vibrio coralliilyticus reveal a diverse virulence repertoire

et al. 2011

View full text Add to dashboard Cite

Vibrio coralliilyticus has been implicated as an important pathogen of coral species worldwide. In this study, the nearly complete genome of Vibrio coralliilyticus strain P1 (LMG23696) was sequenced and proteases implicated in virulence of the strain were specifically investigated. The genome sequence of P1 (5 513 256 bp in size) consisted of 5222 coding sequences and 58 RNA genes (53 tRNAs and at least 5 rRNAs). Seventeen metalloprotease and effector (vgrG, hlyA and hcp) genes were identified in the genome and expressed proteases were also detected in the secretome of P1. As the VcpA zinc-metalloprotease has been considered an important virulence factor of V. coralliilyticus, a vcpA deletion mutant was constructed to evaluate the effect of this gene in animal pathogenesis. Both wild-type and mutant (DvcpA) strains exhibited similar virulence characteristics that resulted in high mortality in Artemia and Drosophila pathogenicity bioassays and strong photosystem II inactivation of the coral dinoflagellate endosymbiont (Symbiodinium). In contrast, the DvcpA mutant demonstrated higher hemolytic activity and secreted 18 proteins not secreted by the wild type. These proteins included four types of metalloproteases, a chitinase, a hemolysin-related protein RbmC, the Hcp protein and 12 hypothetical proteins. Overall, the results of this study indicate that V. coralliilyticus strain P1 has a diverse virulence repertoire that possibly enables this bacterium to be an efficient animal pathogen.

show abstract

“…However, a few members possess two reactive sites that simultaneously bind two protease molecules and are thus termed double-headed inhibitors (15-18). All of these inhibitors are classified into family I3 of peptidase inhibitors (19). Most members are further grouped into subfamily I3A.…”

mentioning

confidence: 99%

The Ternary Structure of the Double-headed Arrowhead Protease Inhibitor API-A Complexed with Two Trypsins Reveals a Novel Reactive Site Conformation

Bao

Zhou

Jiang

et al. 2009

Journal of Biological Chemistry

View full text Add to dashboard Cite

The double-headed arrowhead protease inhibitors API-A and -B from the tubers of Sagittaria sagittifolia (Linn) feature two distinct reactive sites, unlike other members of their family. Although the two inhibitors have been extensively characterized, the identities of the two P1 residues in both API-A and -B remain controversial. The crystal structure of a ternary complex at 2.48 Å resolution revealed that the two trypsins bind on opposite sides of API-A and are 34 Å apart. The overall fold of API-A belongs to the ␤-trefoil fold and resembles that of the soybean Kunitz-type trypsin inhibitors. The two P1 residues were unambiguously assigned as Leu 87 and Lys 145 , and their identities were further confirmed by site-directed mutagenesis. Reactive site 1, composed of residues P5 Met 83 to P5 Ala 92 , adopts a novel conformation with the Leu 87 completely embedded in the S1 pocket even though it is an unfavorable P1 residue for trypsin. Reactive site 2, consisting of residues P5 Cys 141 to P5 Glu 150 , binds trypsin in the classic mode by employing a two-disulfide-bonded loop. Analysis of the two binding interfaces sheds light on atomic details of the inhibitor specificity and also promises potential improvements in enzyme activity by engineering of the reactive sites.Protease inhibitors (PIs) 4 are ubiquitously distributed in all organisms, including plants, animals, and microorganisms (1). They play vital roles in regulating their corresponding proteases, which are involved in many biological processes such as protein digestion, cell signal transmission, inflammation, apoptosis, blood coagulation, and embryogenesis (2). The clinical applications of PIs are widespread, and there is great interest in developing more potent therapeutic PIs for treating human diseases related to cancer (3), pancreatitis (4), thrombosis (5), and AIDS (6). To this end, the soybean Kunitz-type serine proteases inhibitors have been extensively studied (1,(7)(8)(9)(10)(11). The inhibitors of this family generally contain 170 -200 residues and have two disulfide bonds. Most members have only one reactive site located in the region of residues 60 -70 (7,10,(12)(13)(14). However, a few members possess two reactive sites that simultaneously bind two protease molecules and are thus termed double-headed inhibitors (15-18). All of these inhibitors are classified into family I3 of peptidase inhibitors (19). Most members are further grouped into subfamily I3A. However, the double-headed arrowhead PIs API-A and -B are grouped in subfamily I3B because of their very low sequence similarity to other members (19). In contrast to other double-headed PIs such as the Bowman-Birk and ovomucoid inhibitors, which have two identical reactive sites that have evolved by domain shuffling and gene duplication (1, 20 -25), both API-A and -B have two distinct reactive sites.API-A and -B were first purified from the tubers of Sagittaria sagittifolia (Linn) in 1979 (26). Both consist of 179 residues with three disulfide bonds and can inhibit a variety of serine pr...

show abstract

Evolutionary families of peptidase inhibitors

Cited by 552 publications

References 105 publications

Structure of a serine protease poised to resynthesize a peptide bond

Structure of a serine protease poised to resynthesize a peptide bond

Genomic and proteomic analyses of the coral pathogen Vibrio coralliilyticus reveal a diverse virulence repertoire

The Ternary Structure of the Double-headed Arrowhead Protease Inhibitor API-A Complexed with Two Trypsins Reveals a Novel Reactive Site Conformation

Contact Info

Product

Resources

About