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PubMed1984

Purification and characterization of trypsin-like enzyme from sea urchin eggs: substrate specificity and physiological role.

A trypsin-like enzyme has been purified to homogeneity from eggs of the sea urchin, Strongylocentrotus intermedius. The purified enzyme efficiently hydrolyzed Z-Phe-Arg-4- methylcoumaryl -7-amide (MCA) and Pro-Phe-Arg-MCA among 12 peptidyl-Arg (or Lys)- MCAs . The substrate specificity of the enzyme was closely similar to that of the enzyme activity in the egg cortical granule exudate. Among various peptidyl-argininal (Arg-H) derivatives, Z-Phe-Arg-H and Z-Phe-Leu-Arg-H showed the strongest inhibition against both the activity of the purified enzyme and the elevation of vitelline coat. Thus, the trypsin-like enzyme of sea urchin possesses a narrow substrate specificity and participates at least in the elevation of vitelline coat during fertilization.

Animals↗

PubMed2003

Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase.

The 3C-like proteinase of severe acute respiratory syndrome (SARS) coronavirus has been proposed to be a key target for structural-based drug design against SARS. In order to understand the active form and the substrate specificity of the enzyme, we have cloned, expressed, and purified SARS 3C-like proteinase. Analytic gel filtration shows a mixture of monomer and dimer at a protein concentration of 4 mg/ml and mostly monomer at 0.2 mg/ml, which correspond to the concentration used in the enzyme assays. The linear decrease of the enzymatic-specific activity with the decrease of enzyme concentration revealed that only the dimeric form is active and the dimeric interface could be targeted for structural-based drug design against SARS 3C-like proteinase. By using a high pressure liquid chromatography assay, SARS 3C-like proteinase was shown to cut the 11 peptides covering all of the 11 cleavage sites on the viral polyprotein with different efficiency. The two peptides corresponding to the two self-cleavage sites are the two with highest cleavage efficiency, whereas peptides with non-canonical residues at P2 or P1' positions react slower. The P2 position of the substrates seems to favor large hydrophobic residues. Secondary structure studies for the peptide substrates revealed that substrates with more beta-sheetlike structure tend to react fast. This study provides a basic understanding of the enzyme catalysis and a full substrate specificity spectrum for SARS 3C-like proteinase, which are helpful for structural-based inhibitor design against SARS and other coronavirus.

Catalysis↗

PubMed1994

Changing the substrate specificity of penicillin G acylase from Kluyvera citrophila through selective pressure.

Escherichia coli (muT, mutD, Leu-) cells transformed with plasmid pYKD59 harbouring the pac gene encoding penicillin acylase (PA) from Kluyvera citrophila ATCC 21285 were exposed to environmental conditions that made expression of this enzyme essential for growth. Under these conditions, spontaneous mutants were isolated that used adipyl-L-leucine as the sole source of L-leucine. DNA sequencing of the mutant pac genes identified a transversion mutation of thymine to guanine at position 1163. This mutation was located in the beta-subunit of the enzyme and resulted in conversion of Phe-360 to valine. The assignment of this mutation to the shift in substrate specificity was further confirmed by site-directed mutagenesis. Secondary-structure prediction of the region surrounding Phe-360 suggests that this mutation should not produce any significant structural change. The purified mutant acylase was able to hydrolyse adipyl-, glutaryl-, valeryl-, caproyl-, heptanoyl- and phenoxyacetyl-L-leucine at pH 5 with greater efficiency than the wild-type enzyme. However, the mutant enzyme was not able to hydrolyse glutaryl-7-aminocephalosporanic acid and had lost 90% and 50% of activity on penicillin G and phenylacetyl-L-leucine respectively. Nevertheless, mutant PA retained its original activity on 6-nitro-3-phenylacetamidobenzoate and p-nitrophenylphenylacetate, suggesting that the binding specificity of PA by the acyl and amine moieties of the substrate are not independent phenomena. The small differences observed between the c.d. spectra of the mutant enzyme recorded at pH 5 and 8 suggest the existence of different conformational states at the two pH values, but these differences were indistinguishable from those observed in the native enzyme and cannot be correlated with the shift in substrate specificity. Our results demonstrate that it is possible to change the specificity of PA by laboratory evolution and use it to identify the amino acids involved in substrate recognition. However, the synchronous participation of the alpha- and beta-subunits in the complex induced-fit-like mechanism of acylases suggests that, to obtain new enzymes for industrial application, the selection pressure should be specifically designed for the compound of interest.

Amino Acid Sequence↗

PubMed1995

Differences in substrate specificity between Cdk2-cyclin A and Cdk2-cyclin E in vitro.

Cyclin-dependent kinase 2 (Cdk2), when bound to either cyclin A or cyclin E, recognizes the Ser/Thr-Pro-X-basic amino acid (motif A) as a phosphorylation site. In this study, we designed several peptides based on motif A and examined the substrate specificity of Cdk2-cyclin A and Cdk2-cyclin E using these peptides. Peptides containing a proline residue in the sequence Pro-X-Thr-Pro-X-basic amino acid (motif B) had higher affinity for both Cdk2 complexes than peptides containing motif A. Furthermore, differences in substrate affinity between the two Cdk2 complexes were caused by a proline residue adjacent to or three positions before the threonine residue. Similarly, the presence of different basic amino acids in motif B also had different effects on affinity for each complex. We demonstrate the possibility that the substrate specificity of Cdk2 bound to cyclin might be regulated by the species of cyclin.

Amino Acid Sequence↗

PubMed2006

X-ray structure of potato epoxide hydrolase sheds light on substrate specificity in plant enzymes.

Epoxide hydrolases catalyze the conversion of epoxides to diols. The known functions of such enzymes include detoxification of xenobiotics, drug metabolism, synthesis of signaling compounds, and intermediary metabolism. In plants, epoxide hydrolases are thought to participate in general defense systems. In the present study, we report the first structure of a plant epoxide hydrolase, one of the four homologous enzymes found in potato. The structure was solved by molecular replacement and refined to a resolution of 1.95 A. Analysis of the structure allows a better understanding of the observed substrate specificities and activity. Further, comparisons with mammalian and fungal epoxide hydrolase structures reported earlier show the basis of differing substrate specificities in the various epoxide hydrolase subfamilies. Most plant enzymes, like the potato epoxide hydrolase, are expected to be monomers with a preference for substrates with long lipid-like substituents of the epoxide ring. The significance of these results in the context of biological roles and industrial applications is discussed.

Crystallography, X-Ray↗

PubMed1990

Substrate specificity of the exonuclease associated with calf DNA polymerase.

The digestion mechanism and substrate specificity of the 3' to 5' exonuclease associated with calf thymus DNA polymerase epsilon have been examined. The use of single-molecule mismatched DNA substrates has allowed further characterization of the structural substrate requirements of the nonprocessive exonucleolytic activity of DNA polymerase epsilon. The digestion characteristics of these substrates demonstrated that a single-stranded segment 5' to the double-stranded complementary region is not a prerequisite for efficient exonucleolytic degradation of the mismatched single-stranded segment at the 3' end of the molecule. In contrast to the known inhibitory effect of DNA polymerase activity at moderate concentration of monovalent ions, the distribution of digestive products was virtually unaffected by the addition of 80 mM KCl to the reaction. Aphidicolin, an inhibitor of DNA polymerase activity, also inhibits exonucleolytic activity on substrates containing a terminal mismatch, while little effect is observed for the digestion of single-stranded DNA substrates. However, if a long terminal mismatched DNA substrate is used to mimic the structure of a single-stranded DNA molecule, the extent of digestion is significantly decreased by the addition of aphidicolin. Inhibition of the digestion of single-stranded DNA by aphidicolin is also observed if a double-stranded complementary region with a 3' single-stranded DNA segment is added to the reaction. These results indicate that aphidicolin inhibits exonuclease activity by sequestering the enzyme to a portion of mismatched DNA molecules away from the site where the exonuclease must act. Additionally, they demonstrate that, although the polymerase and exonuclease active sites are structurally linked, polymerase function is not a necessary requirement for exonuclease function.

Animals↗

PubMed1993

Protein kinase C isotypes and signal-transduction in human neutrophils: selective substrate specificity of calcium-dependent beta-PKC and novel calcium-independent nPKC.

Neutrophils possess at least two phospholipid-dependent forms of protein kinase C, a classical Ca/PS/DG-dependent beta-isotype of protein kinase C and a Ca-independent but PS/DG-dependent novel protein kinase C (nPKC) which we now demonstrate to have different substrate specificities. Activation of human neutrophils triggers assembly of an NADPH oxidase in the membrane and generation of O2-. A role for the major Ca-dependent isotype beta-PKC in neutrophils is proposed in stimulus-induced phosphorylation and association of a cytosolic 47 kDa protein (p47-phox) with the membrane NADPH oxidase. In this study we demonstrate that purified beta-PKC and nPKC have very different substrate specificities; beta-PKC but not nPKC phosphorylated both endogenous and recombinant p47-phox. In addition, beta-PKC but not nPKC phosphorylated [ser25]PKC(19-31), the substrate peptide based on a sequence in the Ca-dependent alpha, beta and gamma-isotypes. Pseudosubstrate(19-36), derived from the C-terminus of Ca-dependent PKC isotypes, inhibited beta-PKC but not nPKC activity using either Histone IIIS or peptide(19-31) as substrate. Pseudosubstrate(19-36) also inhibited beta-PKC catalyzed phosphorylation of endogenous and recombinant p47-phox. Pseudosubstrate(19-36) also inhibited the O2- generation triggered by GTP gamma S in electroporated neutrophils by 50%. 32P-Labelled neutrophils electroporated in the presence of GTP gamma S showed phosphorylation of multiple cytosolic proteins including a 47 kDa band, and phosphorylation of membrane-associated 34 kDa, 47 kDa and 54 kDa proteins. Pseudosubstrate(19-36) inhibited phosphorylation of p47-phox in the membrane but not in the cytosol. These findings suggest translocatable, Ca-dependent isotypes of PKC such as beta-PKC may play a role in the phosphorylation of membrane associated p47-phox and the assembly or maintenance of an active NADPH oxidase.

Calcium↗

PubMed1998

Substrate specificity of the alpha-L-arabinofuranosidase from Trichoderma reesei.

The precise substrate specificities of an alpha-L-arabinofuranosidase from Trichoderma reesei were investigated. The enzyme released arabinose at appreciable rates from p-nitrophenyl-alpha-L-arabinofuranoside, O-alpha-L-arabinofuranosyl-(1-->3)-O-beta-D-xylopyranosyl-(1-->4) -D-xylopyranose (A1X2), arabinan, arabinoxylan, arabinogalactan, debranched-arabinan and gum arabic, but not from O-beta-D-xylopyranosyl-(1-->4)-[O-alpha-L-arabinofuranosyl-(1-->3)] -O-beta-D-xylopyranosyl-(1-->4)-D-xylopyranose (A1X3) or O-beta-D-xylopyranosyl-(1-->2)-O-alpha-L-arabinofuranosyl -(1-->3)-O-beta-D-xylopyranosyl-(1-->4)-O-beta-D-xylopyranosyl-(-->4) -D-xylopyranose (A1X4). The enzyme hydrolyzed methyl 2-O-, methyl 3-O- and methyl 5-O-alpha-L-arabinofuranosyl-alpha-L-arabinofuranosides to arabinose and methyl alpha-L-arabinofuranoside with the order of hydrolysis being: (1-->5)- > (1-->2)- > or = (1-->3)-linkages. The enzyme hydrolyzed the (1-->3)-linkage faster than the (1-->5)-linkage of methyl 3,5-di-O-alpha-L-arabinofuranosyl-alpha-L-arabinofuranoside. The degree of conversion of arabinan and debranched-arabinan to monosaccharides by the enzyme was 33.0% and 9.1%, respectively. The alpha-L-arabinofuranosidase preferentially cleaved the arabinosyl side-chain from the arabinan rather than the terminal arabinosyl residue of the arabinan backbone.

Carbohydrate Conformation↗

PubMed2000

Determinants of substrate specificity of a second non-neuronal secreted acetylcholinesterase from the parasitic nematode Nippostrongylus brasiliensis.

We recently reported on a non-neuronal secreted acetylcholinesterase (AChE B) from the nematode parasite Nippostrongylus brasiliensis. Here we describe the primary structure and enzymatic properties of a second secreted variant, termed AChE C after the designation of native AChE isoforms from this parasite. As for the former enzyme, AChE C is truncated at the carboxyl terminus in comparison with the Torpedo AChE, and three of the 14 aromatic residues that line the active site gorge are substituted by nonaromatic residues, corresponding to Tyr70 (Ser), Trp279 (Asn) and Phe288 (Met). A recombinant form of AChE C was highly expressed by Pichia pastoris. The enzyme was monomeric and hydrophilic, and displayed a marked preference for acetylthiocholine as substrate. A double mutation (W302F/W345F, corresponding to positions 290 and 331 in Torpedo) rendered the enzyme 10-fold less sensitive to excess substrate inhibition and two times less susceptible to the bis quaternary inhibitor BW284C51, but did not radically affect substrate specificity or sensitivity to the 'peripheral site' inhibitor propidium iodide. In contrast, a triple mutant (M300G/W302F/W345F) efficiently hydrolysed propionylthiocholine and butyrylthiocholine in addition to acetylthiocholine, while remaining insensitive to the butyrylcholinesterase-specific inhibitor iso-OMPA and displaying a similar profile of excess substrate inhibition as the double mutant. These data highlight a conserved pattern of active site architecture for nematode secreted AChEs characterized to date, and provide an explanation for the substrate specificity that might otherwise appear inconsistent with the primary structure in comparison to other invertebrate AChEs.

Acetylcholinesterase↗

PubMed1977

Substrate-induced conformational changes in lactate dehydrogenase. Proteolysis of the immobilized enzyme in the presence of specific substrates.

We report here a new approach to the study of the conformation of enzymes in the presence of specific substrates. Rabbit muscle lactate dehydrogenase was attached to CL-Sepharose via a cleavable spacer arm (-NH-(CH2)6NHCO(CH2)2SS(CH2)2CO-). The bound lactate dehydrogenase was digested with subtilisin BPN' in the presence of substrates of lactate dehydrogenase. The use of a flow system permits the maintenance of saturating levels of substrates. Proteolysis was followed by loss of activity of the enzyme column. The time course of proteolysis in the presence of either NADH, NAD+, or pyruvate alone did not differ from the control. However, when NADH and pyruvate were present simultaneously, the enzyme became more susceptible to proteolysis. The initial rate of proteolysis was increased by 40%. The abortive ternary complex (lactate dehydrogenase - NAD+ - pyruvate) also showed an increase in susceptibility to proteolysis. These findings clearly show that the productive ternary complex (lactate dehydrogenase - NADH - pyruvate) is conformationally different from the apoenzyme and binary complexes under optimal catalytic conditions.

Enzymes, Immobilized↗

PubMed1981

A specific substrate from rabbit cerebellum for guanosine-3':5'-monophosphate-dependent protein kinase. III. Amino acid sequences at the two phosphorylation sites.

G-substrate is a protein present in cerebellum which is a major endogenous substrate for cyclic GMP-dependent protein kinase, and one of the few known proteins phosphorylated more effectively by cyclic GMP-dependent protein kinase than by cyclic AMP-dependent protein kinase. G-substrate has been shown to be phosphorylated on two threonine residues, and the amino acid sequences surrounding these sites, which correspond to about 30% of the primary structure, are: Leu-Asn-Val-Glu-Ser-Asp-Gln-Lys-Lys-Pro-Arg-Arg-Lys-Asp-Thr(P)-Pro-Ala-Leu-His- Ile-Pro-Pro-Phe-Ile-Ser-Gly-Val-Ile-Ser-Gln-Asn SITE 1 Leu-His-Asn-Thr-Asp-Leu-Glu-Gln-Gln-Lys-Pro-Arg-Arg-Lys-Asp-Thr(P)-Pro-Ala-Leu- His-Thr-Ser-Pro-Phe-Gln-Ser-Gly-Val-Arg SITE 2 The amino acid sequences surrounding the phosphorylated residues show 18 identities over a sequence of 26 residues, and suggest that G-substrate contains an internal gene duplication. Site-1 appears to be located 17 residues from the COOH terminus of the protein. Site 1 and site 2 are phosphorylated at similar rates by cyclic GMP-dependent protein kinase. In contrast, cyclic AMP-dependent protein kinase phosphorylates site 1 4-fold more rapidly than site 2. A decapeptide sequence surrounding the phosphothreonine residues in G-substrate shows 5 identities with that surrounding the phosphothreonine residue in protein phosphatase inhibitor 1. Inhibitor 1, a specific substrate for cyclic AMP-dependent protein kinase, also resembles G-substrate in its physical properties. The possible function of G-substrate and the molecular specificities of cyclic AMP-dependent protein kinase and cyclic GMP-dependent protein kinase are discussed in the light of these results.

Amino Acid Sequence↗

PubMed2005

Purification, properties and alternate substrate specificities of arginase from two different sources: Vigna catjang cotyledon and buffalo liver.

Arginase was purified from Vigna catjang cotyledons and buffalo liver by chromatographic separations using Bio-Gel P-150, DEAE-cellulose and arginine AH Sepharose 4B affinity columns. The native molecular weight of an enzyme estimated on Bio-Gel P-300 column for Vigna catjang was 210 kDa and 120 kDa of buffalo liver, while SDS-PAGE showed a single band of molecular weight 52 kDa for cotyledon and 43 kDa for buffalo liver arginase. The kinetic properties determined for the purified cotyledon and liver arginase showed an optimum pH of 10.0 and pH 9.2 respectively. Optimal cofactor Mn(++) ion concentration was found to be 0.6 mM for cotyledon and 2 mM for liver arginase. The Michaelis-Menten constant for cotyledon arginase and hepatic arginase were found to be 42 mM and 2 mM respectively. The activity of guanidino compounds as alternate substrates for Vigna catjang cotyledon and buffalo liver arginase is critically dependent on the length of the amino acid side chain and the number of carbon atoms. In addition to L-arginine cotyledon arginase showed substrate specificity towards agmatine and L-canavanine, whereas the liver arginase showed substrate specificity towards only L-canavanine.

Animals↗

PubMed1975

[Substrate specifity of "cholesteroloxidase" for the enzymatic determination of cholesterol].

The substrate specifity of "Cholesteroloxidase" (E.C.1.1.3.6) from Nocardia erythropolis was studied. The main sterols from animal and plant fats and 4-methylsterols as well as one triterpene served as substrates. The enzyme is not specific for cholesterol but also reacts with all the natural 3 beta-hydroxysterols. However, the enzymatic reaction may contribute as a new analytical method to determine the "total sterols" in the unsaponifiable matter of fats.

Alcohol Oxidoreductases↗

PubMed1990

Substrate specificity of the protease that processes human interleukin-1 beta.

The substrate specificity of the protease which generates mature human interleukin-1 beta (IL-1 beta) from pro-interleukin-1 beta was investigated using synthetic peptide substrates and recombinant pro-IL-1 beta. The requirement of an L-aspartate in the P-1 position was confirmed together with the need for a small hydrophobic residue in the P-1' position (Gly or Ala). It was shown that the enzyme can tolerate conservative substitutions in the P-2 and P-2' positions. We found little difference in the enzyme's ability to cleave denatured and native pro-IL-1 beta, indicating that tertiary structure recognition is not involved in binding. The enzyme did, however, require a peptide of more than six amino acids for cleavage to occur. These results conclusively demonstrate the unusual specificity of this protease.

Amino Acid Sequence↗

PubMed2006

A loop of coagulation factor VIIa influencing macromolecular substrate specificity.

Coagulation factor VIIa (FVIIa) belongs to a family of proteases being part of the stepwise, self-amplifying blood coagulation cascade. To investigate the impact of the mutation Met(298{156})Lys in FVIIa, we replaced the Gly(283{140})-Met(298{156}) loop with the corresponding loop of factor Xa. The resulting variant exhibited increased intrinsic activity, concurrent with maturation of the active site, a less accessible N-terminus, and, interestingly, an altered macromolecular substrate specificity reflected in an increased ability to cleave factor IX (FIX) and a decreased rate of FX activation compared to that of wild-type FVIIa. In complex with tissue factor, activation of FIX, but not of FX, returned to normal. Deconvolution of the loop graft in order to identify important side chain substitutions resulted in the mutant Val(158{21})Asp/Leu(287{144})Thr/Ala(294{152})Ser/Glu(296{154}) Ile/Met(298{156})Lys-FVIIa with almost the same activity and specificity profile. We conclude that a lysine residue in position 298{156} of FVIIa requires a hydrophilic environment to be fully accommodated. This position appears critical for substrate specificity among the proteases of the blood coagulation cascade due to its prominent position in the macromolecular exosite and possibly via its interaction with the corresponding position in the substrate (i.e. FIX or FX).

Amino Acid Substitution↗

PubMed1980

Substrate-specificity studies on protochlorophyllide reductase in barley (Hordeum vulgare) etioplast membranes.

1. The substrate specificity of the enzyme protochlorophyllide reductase in barley (Hordeum vulgare) etioplasts was investigated. 2. It was shown that naturally occurring esterified protochlorophyllide and chemically prepared protochlorophyllide methyl ester are not substrates for the enzyme, suggesting an important role for the C-7 carboxylic acid group in binding of the porphyrin to the enzyme. 3. Removal of magnesium from the protochlorophyllide leads to inactivity of the compound as a substrate for the enzyme. However, activity can be restored by replacing the magnesium with zinc, whereas nickel, copper or cobalt failed to restore substrate activity. 4. Binding of the second substrate, NADPH, to the enzyme probably occurs through the 2'-phosphate group in the coenzyme.

Chloroplasts↗

PubMed1997

8-hydroxyguanine (7,8-dihydro-8-oxoguanine) DNA glycosylase and AP lyase activities of hOGG1 protein and their substrate specificity.

Recently we cloned a structural human homolog (hOGG1) of the yeast OGG1 (yOGG1) gene that is involved in the excision repair of 8-hydroxyguanine (also known as 7,8-dihydro-8-oxoguanine; oh8Gua), hOGG1 protein shares 38% amino acid identity with yOGG1 protein. In this paper, we define the substrate specificity of oh8Gua DNA glycosylase and AP lyase activities of the hOGG1 protein. The oh8Gua released from oh8Gua containing DNA was measured by analysis with HPLC coupled with electrochemical detector (ECD) and cleavage sites in the DNA were identified by cleavage assay using gel electrophoresis. GST-hOGG1 protein possessed the oh8Gua DNA glycosylase/AP lyase activity and weak delta-elimination activity, oh8Gua opposite the C in duplex oligonucleotide was most efficiently released by GST-hOGG1 protein and oh8Gua opposite the T was also released, while oh8Gua opposite the G or A was very slowly done. The rank order of DNA cleavage efficiency was the same as that of oh8Gua glycosylase activity. Glycosylase/AP lyase activities and their substrate specificities of the GST-hOGG1 protein was similar to GST-yOGG1 protein but different from MutM protein. These results indicate that the dominant function of hOGG1 protein is a oh8Gua glycosylase reaction by specifically recognizing oh8Gua and pyrimidine opposite the oh8Gua and delta-elimination reaction in the same manner as yOGG1 protein. Thus, the hOGG1 gene is a functional human homolog of the yOGG1 gene on oh8Gua excision repair in spite of the low structural identity at amino acid level between hOGG1 and yOGG1 proteins.

8-Hydroxy-2'-Deoxyguanosine↗

PubMed2005

Analysis of substrate specificity and endopeptidyl activities of the cathepsin B-like proteinase from Helicoverpa armigera.

The cathepsin B-like proteinase from Helicoverpa armigera (HCB) is involved in the degradation of yolk proteins during embryonic development. In order to gain insight into the substrate specificity of this proteinase, various proteins from animals and plants were tested as substrates. The specific cleavage sites of this enzyme on endopeptide bonds were assayed using bovine serum albumin (BSA) as a substrate. Results showed that BSA was degraded into several fragments, which suggests that HCB cleaves BSA at specific endopeptidyl sites. The amino acid sequences of the BSA derived peptides were determined, revealing cleavage of the bonds between residues Arg81-Glu82, Val423-Glu424 and Gly430-Lys431. This suggests that the minimum requirement for a scissile bond to be recognized by HCB is the presence of an ionic amino acid at the P1 ' position and the P1 position can vary. These observations suggest that HCB cleaves bonds at the N-terminal side of ionic amino acid residues giving HCB a wide range of substrates, though other factors dictating the substrate specificity of this enzyme remains to be clarified. Our results provide new evidence that HCB functions as an endopeptidase on some proteins.

Amino Acid Sequence↗