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PubMed1988

QSAR analysis of the subtilisin hydrolysis of X-phenyl hippurates. II. A study of subtilisin BPN'.

The hydrolysis of 30 substituted phenyl hippurates (X-C6H4OCOCH2NHCOC6H5) by subtilisin BPN' was studied and from the results the following quantitative structure-activity relationship was derived: log 1/Km = 0.39 sigma + 0.16 B5.4 + 0.29 pi'3 + 3.58. In this expression Km is the Michaelis constant, sigma is the Hammett constant, B5.4 is the sterimol steric parameter of X in the 4-position and pi'3 is the hydrophobic parameter for the more hydrophobic of the two possible meta substituents. The other meta substitutent is assigned a pi value of 0. This mathematical model is qualitatively compared with a molecular graphics model constructed from the X-ray crystallographic coordinates of subtilisin BPN'. The results with subtilisin BPN' are compared with our earlier study of similar substrates with Carlsberg subtilisin.

Computer Graphics↗
PubMed1994

Achievement of renaturation of subtilisin BPN' by a novel procedure using organic salts and a digestible mutant of Streptomyces subtilisin inhibitor.

The pro-sequences of proteases have been considered to be required for the refolding of denatured proteases. However, here we report achievement of almost complete restoration of enzymatic activity of subtilisin BPN' in the absence of its pro-sequence. The presence of 2 M potassium acetate in the folding medium enhanced the refolding efficiency of guanidine hydrochloride (GdnHCl)-denatured subtilisin BPN' by up to 28%, and other organic salts were also found to be useful, suggesting that general contribution of the bulky hydrophobic moieties of the salts to the formation of a favorable environment required for folding. This finding will provide new insights into the folding mechanisms not only of proteases but also of various other proteins. Almost complete restoration of enzymatic activity of denatured subtilisin in the organic salt solution was accomplished by further addition of mutated Streptomyces subtilisin inhibitor (SSI), which had been converted to a digestible temporary inhibitor by removal of the disulfide bridge near the reactive site.

Acetates↗
PubMed1984

Crystal structure at 2.6 A resolution of the complex of subtilisin BPN' with streptomyces subtilisin inhibitor.

The crystal structure of the complex of a bacterial alkaline serine proteinase, subtilisin BPN', with its proteinaceous inhibitor SSI (Streptomyces subtilisin inhibitor) was solved at 2.6 A resolution. Compared with other similar complexes involving serine proteinases of the trypsin family, the present structure is unique in several respects. (1) In addition to the usual antiparallel beta-sheet involving the P1, P2 and P3 residues of the inhibitor, the P4, P5 and P6 residues form an antiparallel beta-sheet with a previously unnoticed chain segment (residues 102 through 104, which was named the S4-6 site) of subtilisin BPN'. (2) The S4-6 site does not exist in serine proteinases of the trypsin family, whether of mammalian or microbial origin. (3) Global induced-fit movement seems to occur on SSI: a channel-like structure in SSI where hydrophobic side-chains are sandwiched between two lobes becomes about 2 A wider upon complexing with subtilisin. (4) The complex is most probably a Michaelis complex, as in most of the other complexes. (5) The main role of the "secondary contact region" of SSI seems to be to support the reactive site loop ("primary contact region"). Steric homology of the two contact regions between the inhibitors of the SSI family and the pancreatic secretory trypsin inhibitor-ovomucoid inhibitor family is so high that it seems to indicate divergent evolutionary processes and to support the general notion as to the relationship of prokaryotic and eukaryotic genes put forward by Doolittle (1978).

Amino Acid Sequence↗
PubMed1992

Functional analysis of the intramolecular chaperone. Mutational hot spots in the subtilisin pro-peptide and a second-site suppressor mutation within the subtilisin molecule.

The N-terminal pro-peptide of 77 amino acid residues is essential for the folding of subtilisin, an alkaline serine protease from Bacillus subtilis. The synthetic pro-peptide has been shown to be capable of guiding the proper folding of denatured subtilisin to enzymatically active enzyme. Thus the pro-peptide serves as an intramolecular chaperone, which is removed by an autoprocessing reaction after the completion of the folding. With use of localized polymerase chain reaction random mutagenesis a total of 25 amino acid substitution mutations that affected subtilisin activities were isolated. These mutations occurred in a high frequency at the hydrophobic regions of the pro-peptide. For one of the mutations, M(-60)T, a second-site suppressor mutation, S(188)L, was isolated within the mature region. These results suggest that the pro-peptide consists of a few functional regions which interact with specific regions of the mature region of subtilisin during the folding process.

Amino Acid Sequence↗
PubMed1977

The stoichiometry of inhibition and binding of a protein proteinase inhibitor from Streptomyces (Streptomyces subtilisin inhibitor) against subtilisin BPN'1.

The stoichiometry of inhibition and binding of Streptomyces subtilisin inhibitor, a protein proteinase inhibitor produced by Streptomyces albogriseolus S-3253 (Sato, S. and Murao, S. (1973) Agric. Biol. Chem. 37, 1067) against subtilison BPN' [EC 3.4.21.14] was studied. The inhibition of the hydrolysis of p-nitrophenyl acetate by subtilisin BPN' was measured both at the pre-steady state with a stopped-flow apparatus and at the steady state. The stopped-flow study demonstrated the disappearance of the initial burst of the enzyme reaction. The ultraviolet absorption difference spectra observed on mixing the inhibitor and the enzyme suggested changes in the environment of tryptophyl and tyrosyl residues in the proteins. Titration by means either of the degree of inhibition at the steady state or of the magnitude of the ultraviolet difference absorbance revealed that the inhibitor (dimer, MW: 23,000) bound and inhibited two molecules of subtilisin BPN'. The inhibitor constant, Ki, against subtilisin BPN' was estimated to be less than 10(-9)M at pH 8.50. The type of inhibition of this inhibitor is discussed.

Bacterial Proteins↗
PubMed1991

Molecular recognition at the active site of subtilisin BPN': crystallographic studies using genetically engineered proteinaceous inhibitor SSI (Streptomyces subtilisin inhibitor).

Unlike trypsin-like serine proteases having only one conspicuous binding pocket in the active site, subtilisin BPN' has two such pockets, the S1 and S4 pockets, which accommodate the P1 and P4 residues of ligands (after Schechter and Berger notation) respectively. Using computer graphics, the geometrical nature of the two pockets was carefully examined and strategies for site-directed mutagenesis studies were set up against a protein SSI (Streptomyces subtilisin inhibitor), which is a strong proteinaceous inhibitor (or a substrate analogue) of subtilisin BPN'. It was decided to convert the P1 residue, methionine 73, into lysine (M73K) with or without additional conversion of the P4 residue, methionine 70, into glycine (M70G). The crystal structures of the two complexes of subtilisin BPN', one with the single mutant SSI (M73K) and the other with the double mutant SSI (M73K, M70G) were solved showing that (i) small 'electrostatic induced-fit movement' occurs in the S1 pocket upon introducing the terminal plus charge of the lysine side chain, and (ii) large 'mechanical induced-fit movement' occurs in the S4 pocket upon reducing the size of the P4 side chain from methionine to glycine. In both (i) and (ii), the induced-fit movement occurred in a concerted fashion involving both the enzyme and 'substrate' amino acid residues. The term 'substrate-assisted stabilization' was coined to stress the cooperative nature of the induced-fit movements.

Bacterial Proteins↗
PubMed1990

Fluorescence labeled and cross-linked subtilisin: kinetic characteristics and binding to Streptomyces subtilisin inhibitor.

In the preceding paper, the preparation of fluorescent cross-linked subtilisin was described. In this paper we present the catalytic and binding properties of the modified enzyme. Kinetic analysis showed that the cross-linked dimeric subtilisin retained both catalytic activity and binding affinity toward synthetic substrates. These kinetic characteristics of the modified enzyme were nearly identical to those of the native enzyme. The modified enzyme also exhibited a specific interaction with Streptomyces subtilisin inhibitor (SSI) with 1 to 1 stoichiometry. The formation of a polymeric complex, which is the expected product with cross-linked subtilisin, was demonstrated.

Bacterial Proteins↗
PubMed1988

Structural comparison of two serine proteinase-protein inhibitor complexes: eglin-c-subtilisin Carlsberg and CI-2-subtilisin Novo.

The crystal structures of the molecular complexes between two serine proteinases and two of their protein inhibitors have been determined: subtilisin Carlsberg with the recombinant form of eglin-c from the leech Hirudo medicinalis and subtilisin Novo with chymotrypsin inhibitor 2 from barley seeds. The structures have been fully refined by restrained-parameter least-squares methods to crystallographic R factors (sigma[[Fo[ - [Fc[[/sigma[Fo[) of 0.136 at 1.8-A resolution and 0.154 at 2.1-A resolution, respectively. The 274 equivalent alpha-carbon atoms of the enzymes superpose with an rms deviation of 0.53 A. Sequence changes between the enzymes result in localized structural adjustments. Functional groups in the active sites superpose with an rms deviation of 0.19 A for 161 equivalent atoms; this close similarity in the conformation of active-site residues provides no obvious reason for known differences in catalytic activity between Carlsberg and Novo. Conformational changes in the active-site region indicate a small induced fit of enzyme and inhibitor. Some conformational differences are observed between equivalent active-site residues of subtilisin Carlsberg and alpha-chymotrypsin. Despite differences in tertiary architecture, most enzyme-substrate (inhibitor) interactions are maintained. Subtilisin Carlsberg has a rare cis-peptide bond preceding Thr211 (Gly211 in Novo). Both enzymes contain tightly bound Ca2+ ions. Site 1 is heptacoordinate with the oxygen atoms at the vertices of a pentagonal bipyramid. Site 2 in Carlsberg is probably occupied by a K+ ion in Novo. Conserved water molecules appear to play important structural roles in the enzyme interior, in the inhibitor beta-sheet, and at the enzyme-inhibitor interface. The 62 equivalent alpha-carbon atoms of the inhibitors superpose with an rms deviation of 1.68 A. Sequence changes result in somewhat different packing of the alpha-helix, beta-sheet, and reactive-site loop relative to each other. Hydrogen bonds and electrostatic interactions supporting the conformation of the reactive-site loop are conserved. The 24 main-chain plus C beta atoms of P4 to P1' overlap with an rms deviation of 0.19 A. Features contributing to the inhibitory nature of eglin-c and CI-2 are discussed.

Amino Acid Sequence↗
PubMed1986

Refined 1.2 A crystal structure of the complex formed between subtilisin Carlsberg and the inhibitor eglin c. Molecular structure of eglin and its detailed interaction with subtilisin.

The crystal structure of the complex formed between eglin c, an elastase inhibitor from the medical leech, and subtilisin Carlsberg has been determined at 1.2 A resolution by a combination of Patterson search methods and isomorphous replacement techniques. The structure has been refined to a crystallographic R-value of 0.18 (8-1.2 A). Eglin consists of a four-stranded beta-sheet with an alpha-helical segment and the protease-binding loop fixed on opposite sides. This loop, which contains the reactive site Leu45I--Asp46I, is mainly held in its conformation by unique electrostatic/hydrogen bond interactions of Thr44I and Asp46I with the side chains of Arg53I and Arg51I which protrude from the hydrophobic core of the molecule. The conformation around the reactive site is similar to that found in other proteinase inhibitors. The nine residues of the binding loop Gly40I--Arg48I are involved in direct contacts with subtilisin. In this interaction, eglin segment Pro42I--Thr44I forms a three-stranded anti-parallel beta-sheet with subtilisin segments Gly100--Gly102 and Ser125--Gly127. The reactive site peptide bond of eglin is intact, and Ser221 OG of the enzyme is 2.81 A apart from the carbonyl carbon.

Amino Acid Sequence↗
PubMed1985

Calorimetric studies of the binding of Streptomyces subtilisin inhibitor to subtilisin of Bacillus subtilis strain N'.

The binding of Streptomyces subtilisin inhibitor (SSI) to subtilisin of Bacillus subtilis strain N' (subtilisin BPN', EC 3.4.21.14) was studied by isothermal calorimetry at pH 7.0 and at various temperatures ranging from 5 to 30 degrees C. Thermodynamic quantities for the binding reaction were derived as a function of temperature by combining the data reported for the dissociation constant with the present calorimetric results. At 25 degrees C, the values are delta G degrees = -57.9 kJ mol-1, delta H = -19.8 kJ mol-1, delta S degree = 0.13 kJ K-1 mol-1, and delta Cp = -1.02 kJ K-1 mol-1. The entropy and the heat capacity changes are discussed in terms of the contributions from the changes in vibrational modes and in hydrophobic interactions.

Bacillus subtilis↗
PubMed1996

Further evidence for the structure of the subtilisin propeptide and for its interactions with mature subtilisin.

Evidence is presented for some secondary structure, very likely alpha-helical, of the propeptide of subtilisin E in aqueous salt solution, as well as for strong intermolecular interactions between the propeptide and the mature sequence both in the processed and unprocessed states (i.e. in prosubtilisin). Prosubtilisin is shown to exist as a dimer according to size exclusion high performance liquid chromatography under nondenaturing conditions; that dimer may be on the autoprocessing pathway. According to such a model, the prosequence of one prosubtilisin molecule is the template for the refolding of the mature sequence of the second, and, in turn, the hydrolytic process is intermolecular as well. Support for such an intermolecular folding model also includes potent slow binding inhibition of subtilisin by the propeptide, specific proteolysis of the propeptide by subtilisin, and evidence for intermolecular processing under a variety of conditions.

Chromatography, High Pressure Liquid↗
PubMed1993

Interaction of subtilisin BPN' and recombinant Streptomyces subtilisin inhibitors with substituted P1 site residues.

Kinetic analysis was performed on the interaction between subtilisin BPN' and recombinant species of a proteinaceous proteinase inhibitor, Streptomyces subtilisin inhibitor (SSI), of which the P1 site amino acid residue, Met73, was replaced by site-directed mutagenesis. The inhibitor constant, Ki, was determined from the residual enzyme activity by using a peptide substrate. The rate constant of binding, kon, and the rate constant of dissociation, koff, were determined from a progress curve of the substrate hydrolysis in the presence of the inhibitor by using newly derived equations. A recombinant SSI in which Met73 was replaced by Ile showed an affinity (1/Ki) toward subtilisin BPN' of only about 7% of that of the wild-type SSI, and the kinetic analysis revealed that the increase of koff was responsible for this difference. The affinity of other SSI mutants in which Met73 was replaced by Glu or Asp decreased significantly as pH became increasingly alkaline. The decrease in the affinity of these recombinants was due to the decrease of kon rather than the increase of koff. Stopped-flow studies revealed that the binding reaction was reconcilable with a two-step mechanism, and the kinetic parameters for each step were obtained for the binding of the enzyme and recombinant SSIs.

Bacterial Proteins↗
PubMed1984

Reaction of azapeptides with chymotrypsin-like enzymes. New inhibitors and active site titrants for chymotrypsin A alpha, subtilisin BPN', subtilisin Carlsberg, and human leukocyte cathepsin G.

A series of new azapeptide p-nitrophenyl esters containing a variety of P1 aza-amino acid residues have been synthesized, and the reaction of these azapeptides with chymotrypsin A alpha, subtilisin BPN', subtilisin Carlsberg, and human leukocyte cathepsin G at pH 4-7 has been studied. These azapeptides were found to be very useful as active site titrants and inhibitors of serine proteases with chymotrypsin-like specificity. Stable acyl derivatives of serine proteases are formed in the reaction with azapeptides and can be used for future crystallographic investigations. The effects of changing the nature of the P1' leaving group (-ONp, -OPh, -OCH2CF3, -OEt) for these azapeptides was also investigated. N-Acetyl-L-alanyl-L-alanyl-alpha-azanorleucine p-nitrophenyl ester can be used as an active site titrant for human leukocyte cathepsin G and N-acetyl-L-alanyl-alpha-azaphenylalanine p-nitrophenyl ester is a suitable titrant for chymotrypsin A alpha, subtilisins, or cathepsin G.

Aza Compounds↗
PubMed2000

Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.

Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.

Alkanesulfonic Acids↗
PubMed1996

Active site binding loop stabilization in the subtilisin inhibitor eglin c: structural and functional studies on specifically designed mutants in complex with subtilisin and the uncomplexed inhibitor.

As known from the x-ray crystal structure in complex with a proteinase and from NMR studies, the serine proteinase inhibitor eglin c has a wedge-like shape with a hydrophobic core and a solvent exposed active site binding loop which is stabilized by a network of non-covalent core-binding loop interactions. Previous studies implied a crucial role of the P1'-residue Asp-46 for binding loop stabilization and high inhibitory potency of eglin c towards serine proteinases such as subtilisin. In the present study, the formation of specific eglin core-binding loop interactions was modulated by replacing the wildtype Asp-46 by asparagine, glutarnate and glutamine. The x-ray crystal structures of these mutants were solved in complex with subtilisin, and the inhibitory potency towards this enzyme was determined. Our results imply a reduction of inhibitory potency with declining core-binding loop interactions. We succeeded in crystallizing free wildtype eglin c. The 1.95 angstroms x-ray crystal structure indicates that the transition from the free to the bound form of eglin is accompanied by a concerted conformational change in the binding loop, implying an induced fit to the accessible enzyme surface. Except for the binding loop domain and a few residues on the surface of eglin, the differences observed between the uncomplexed and bound form of the inhibitor are only small.

Binding Sites↗
PubMed1991

Stoichiometric complexation of Streptomyces subtilisin inhibitor and subtilisin.

Subtilisin (Sbt) and Streptomyces subtilisin inhibitor (SSI) were analyzed either alone or together using sodium dodecylsulfate (SDS)-polyacrylamide gel electrophoresis (PAGE). With all ratios of Sbt to SSI tested, the proteins formed a stoichiometric complex, and migrated abnormally at the top of the gel. Electroblotting and amino acid sequence analysis of the complex band showed both Sbt and SSI present at approximately equal molar ratios. When excess Sbt was present, it migrated as a free but still folded form slightly above the band corresponding to the complex. When excess SSI was present, it migrated as several species with molecular weights smaller than the intact form; in fact, the sequences of some of these species indicated that they lacked different amounts of N-terminal and possibly C-terminal residues.

Bacterial Proteins↗
PubMed2000

Maturation and specificity of Plasmodium falciparum subtilisin-like protease-1, a malaria merozoite subtilisin-like serine protease.

Plasmodium falciparum subtilisin-like protease-1 (PfSUB-1) is a protein belonging to the subtilisin-like superfamily of serine proteases (subtilases). PfSUB-1 undergoes extensive posttranslational proteolytic processing. The primary translation product is converted in the parasite endoplasmic reticulum to p54. This is further processed to p47, which accumulates in secretory organelles within the merozoite. Here, we present a detailed study of this processing. In vitro translated PfSUB-1 showed no capacity to undergo autocatalytic processing. However, parasite extracts contain a protease that cleaves the in vitro translated proprotein between Asp(219) and Asn(220) to form two products of 31 (p31) and 54 kDa; the latter was indistinguishable from authentic p54 and remained complexed with p31 in a noncovalent interaction characteristic of that between a subtilase prodomain and its cognate catalytic domain. Cross-linking studies showed that this complex also exists in the parasite. Expression of PfSUB-1 in recombinant baculovirus also resulted in processing to p54. Mutation of the predicted active site serine abolished processing. Recombinant p54 was secreted in a complex with p31, and could be further converted to p47 in vitro. Conversion required calcium, was an intramolecular autocatalytic process, and involved a second cleavage between Asp(251) and Ala(252). A decapeptide based on sequence flanking Asp(219) was efficiently cleaved by recombinant PfSUB-1. We conclude that PfSUB-1 is a subtilase with an unusual substrate specificity and that it is activated by two autocatalytic processing steps.

Amino Acid Sequence↗
PubMed1978

Direct fluorometric determination of a dissociation constant as low as 10(-10) M for the subtilisin BPN'--protein proteinase inhibitor (Streptomyces subtilisin inhibitor) complex by a single photon counting technique.

It was found that an increase in fluorescence intensity at 340 nm is observed on the binding of Streptomyces subtilisin inhibitor (SSI) with subtilisin BPN' in the pH range 6--10. The dissociation constant, Ki, of the enzyme-inhibitor complex was determined as a function of pH and temperature by direct fluorometric titration utilizing the single photon counting technique in the protein concentration range of 10(-9) M. Ki values as low as 10(-10) M could be obtained with reasonable accuracy by this high-sensitivity detection method. From the temperature dependence of Ki, it was found that the binding is endothermic, and is entirely "entropy-driven" in nature. The effect of pH on Ki suggested the participation of an ionizable group with pKapp = 8.5 in the binding.

Bacterial Proteins↗