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PubMed1986

Dependence of the substrate specificity and kinetic mechanism of horse-liver alcohol dehydrogenase on the size of the C-3 pyridinium substituent. 3-Benzoylpyridine-adenine dinucleotide.

The kinetic mechanism and the substrate specificity of liver alcohol dehydrogenase are changed when 3-benzoylpyridine-adenine dinucleotide is used as coenzyme. Only primary alcohols are substrates of the enzyme and with ethanol the mechanism becomes rapid-equilibrium random bi-bi. According to model building experiments on a graphic display, the benzoyl group partially enters the substrate binding site, whereas the essential interactions between coenzyme and enzyme are preserved. This restraint on the substrate binding site provides a molecular explanation for the observed dependence between coenzyme and substrate chemical structures.

Alcohol Dehydrogenase↗
PubMed1976

Substrate-specific enzyme variation in natural populations of Drosophila pseudoobscura.

By using a number of different alcohols as substrates, eight alcohol dehydrogenase loci were discovered in Drosophila pseudoobscura. Each of these loci can take more than one substrate. Several of these loci differed in their tissue specificities and activity patterns during development. The genic variation in natural populations was studied at four of these loci and three of them were polymorphic. A quantitative study of substrate-specific differences among alleles of the same locus produced negative results. This result appears to be typical of most studies done on this aspect. From this it was concluded that the substrate specificity of enzymes is not an important factor in determining the greater amount of genic variation at Group II loci than at Group I loci, as proposed by KOJIMA, GILLESPIE and TOBARI (1970). There are several observations which suggest a different explanation for the differences in the genic variability at Group I and Group II loci: (1) There are, on an average, more isozyme loci (loci with similar substrate specificity) for enzymes in Group II than in Group I; (2) The null alleles are far more common at Group II loci than at Group I loci; (3) There is significant heterogeneity in the number of alleles and the heterozygosities at loci within each of these two groups of enzymes; (4) Relatively higher levels of genic variation are observed at Group II loci even in populations which appear to be living in homogeneous environments; and (5) Some loci (e.g. esterases) are highly polymorphic in most species investigated by gel electrophoresis techniques. Based on these general observations, it is proposed that (1) the substrate-specific differences are between isozyme loci and not between alleles of a given locus, and (2) neutral alleles are proportionately far more common at loci at Group II than at loci in Group I, because the former is under less selection constraint than the latter.

Alcohol Oxidoreductases↗
PubMed2006

Substrate specificity of Arabidopsis 3-ketoacyl-CoA synthases.

The very long chain fatty acids (VLCFA) incorporated into plant lipids are derived from the iterative addition of C2 units provided by malonyl-CoA to an acyl-CoA by the 3-ketoacyl-CoA synthase (KCS) component of a fatty acid elongase (FAE) complex. Mining of the Arabidopsis genome sequence database revealed 20 genes with homology to seed-specific FAE1 KCS. Eight of the 20 putative KCSs were cloned, expressed in yeast, and isolated as (His)6 fusion proteins. Five of the eight (At1g71160, At1g19440, At1g07720, At5g04530, and At4g34250) had little or no activity with C16 to C20 substrates while three demonstrated activity with C16, C18, and C20 saturated acyl-CoA substrates. At1g01120 KCS (KCS1) and At2g26640 KCS had broad substrate specificities when assayed with saturated and mono-unsaturated C16 to C24 acyl-CoAs while At4g34510 KCS was specific for saturated fatty acyl-CoA substrates.

3-Oxoacyl-(Acyl-Carrier-Protein) Synthase↗
PubMed1986

Homogeneous uridine kinase from Ehrlich ascites tumor: substrate specificity and inhibition by bisubstrate analogs.

Uridine kinase has been purified to homogeneity from Ehrlich ascites tumor cells. For the phosphate acceptor site, the enzyme shows substrate specificity only for ribopyrimidine nucleosides and is active with various analogs that have limited structural alterations; both endocyclic and exocyclic substituents can be acceptable. Of nucleosides that have been used in the chemotherapy of cancer, 5-fluorouridine, 6-azauridine, and 3-deazauridine are good substrates, whereas arabinosylcytosine is a poor substrate. No analogs are better substrates than the physiological substrates uridine and cytidine. 5', 5''' -P1, P4-Bisnucleoside oligophosphate bisubstrate analogs (e.g., Ap4U, Ap5U) were synthesized and tested as inhibitors. The most effective compound was Ap4U; with a Ki of 197 microM, it bound more tightly than ATP but no better than uridine. Ap3A, Ap4A, and Ap5A were also tested, with the result that both Ap4A and Ap4U were most effective, suggesting that this size of bisubstrate analog most closely approaches the spacing of the catalytic site.

Adenine Nucleotides↗
PubMed2005

Study on substrate specificity at subsites for severe acute respiratory syndrome coronavirus 3CL protease.

Autocleavage assay and peptide-based cleavage assay were used to study the substrate specificity of 3CL protease from the severe acute respiratory syndrome coronavirus. It was found that the recognition between the enzyme and its substrates involved many positions in the substrate, at least including residues from P4 to P2'. The deletion of either P4 or P2' residue in the substrate would decrease its cleavage efficiency dramatically. In contrast to the previous suggestion that only small residues in substrate could be accommodated to the S1' subsite, we have found that bulky residues such as Tyr and Trp were also acceptable. In addition, based on both peptide-based assay and autocleavage assay, Ile at the P1' position could not be hydrolyzed, but the mutant L27A could hydrolyze the Ile peptide fragment. It suggested that there was a stereo hindrance between the S1' subsite and the side chain of Ile in the substrate. All 20 amino acids except Pro could be the residue at the P2' position in the substrate, but the cleavage efficiencies were clearly different. The specificity information of the enzyme is helpful for potent anti-virus inhibitor design and useful for other coronavirus studies.

Amino Acid Sequence↗
PubMed1993

Rabbit liver microsomal endopeptidase with substrate specificity for processing proproteins is structurally related to rat testes metalloendopeptidase 24.15.

The detergent extract of rabbit liver microsomes contains an endopeptidase (MEP) with substrate specificity for peptides containing Arg residues at the P1 and P4 positions in the cleavage site (Kawabata, S., and Davie, E. W. (1992) J. Biol. Chem. 267, 10331-10336). These sequences occur in many proproteins such as the vitamin K-dependent proproteins and prohormones. A cDNA coding for MEP has been obtained from three overlapping clones isolated from two rabbit liver lambda gt10 cDNA libraries. The longest open reading frame of the 3507-base pair cDNA codes for a protein of 704 amino acids, of which 406 residues were confirmed by amino acid sequence analysis. MEP contains a putative active site of -His-Glu-X-X-His-, which is typical of mammalian zinc metallopeptidases. Based on a hydropathy plot, MEP is a hydrophilic protein with no transmembrane domain and no NH2-terminal signal sequence. Amino acid sequence analysis identified Asn at the three potential N-glycosylation sites in the enzyme, indicating that MEP contains no N-linked sugar. MEP is homologous with rat testes metalloendopeptidase 24.15 (60% identity), rat mitochondrial intermediate peptidase (24% identity), Escherichia coli dipeptidyl carboxypeptidase (25% identity), and the open reading frame YCL57w present in yeast chromosome III (35% identity).

Amino Acid Sequence↗
PubMed2006

Evolving the substrate specificity of O6-alkylguanine-DNA alkyltransferase through loop insertion for applications in molecular imaging.

We introduce a strategy for evolving protein substrate specificity by the insertion of random amino acid loops into the protein backbone. Application of this strategy to human O6-alkylguanine-DNA alkyltransferase (AGT) led to the isolation of mutants that react with the non-natural substrate O6-propargylguanine. Libraries generated by conventional random or targeted saturation mutagenesis, by contrast, did not yield any mutants with activity towards this new substrate. The strategy of loop insertion to alter enzyme specificity should be general and applicable to other classes of proteins. An important application of the isolated AGT mutant is in molecular imaging, where the mutant and parental AGTs are used to label two different AGT fusion proteins with different fluorophores in the same living cell or in vitro . This allowed the establishment of fluorescence-based assays to detect protein-protein interactions and measure enzymatic activities.

Amino Acid Sequence↗
PubMed1997

Substrate specificity of carp Cyprinus carpio cathepsin H with methylcoumarylamide substrates.

Cathepsin H was purified from the crude extract of carp (Cyprinus carpio) hepatopancreas by a reformed method involving six stages, and the specific activity increased about 11,500-fold with a 23% recovery. Of varying fluorescent synthetic substrates tested, carp cathepsin H possessed an ability to hydrolyze four N-terminal unblocked substrates those are composed of a single amino acid bound to 4-methylcoumaryl-7-amide (MCA), namely Leu-MCA, Arg-MCA, Lys-MCA and Ala-MCA. In contrast the enzyme was only marginally able to hydrolyze an unblocked substrate such as Pro-Phe-Arg-MCA and totally unable to degrade all blocked derivative employed. From the kinetic constants with four unblocked substrates, car cathepsin H had the highest affinity toward Leu-MCA with a Km value of 35.4 microM. Besides both the hydrolytic rates and molecular activities of the enzyme decreased from Lys-MCA > Arg-MCA > Ala-MCA > Leu MCA as judged by their Vmax and Kcat values, respectively. Otherwise, optimal pHs for hydrolysis of cathepsin H were different for four substrates. The enzyme exhibited maximum level of the activity at pH 6.5 for Arg-MCA and Lys-MCA and at pH 7.0 for Leu-MCA and Ala-MCA.

Animals↗
PubMed1991

New enzymes for old: redesigning the coenzyme and substrate specificities of glutathione reductase.

A set of amino acid side chains that confer specificity for the coenzyme NADPH and the substrate glutathione in the flavoprotein disulphide oxidoreductase, glutathione reductase, has been identified. Systematic replacement of these amino acid residues in the coenzyme-binding site switches the specificity of the enzyme from its natural strong preference for NADPH to a marked preference for NADH. The amino acids replaced all lie in a structural motif within the dinucleotide-binding domain of the protein. Since this domain is a feature common to most dehydrogenases (reductases) that use nicotinamide coenzymes, it may be that the coenzyme specificities of all such enzymes can be manipulated in this way. Similarly, amino acid residues involved in the selective recognition of trypanothione by trypanothione reductase, an enzyme related to glutathione reductase and exclusive to trypanosomatids, were identified. Suitable mutation of the corresponding residues in E. coli glutathione reductase switched its substrate specificity towards trypanothione. A better understanding of the substrate specificity of these enzymes could open up a route to the chemotherapy of trypanosomal infections.

Amino Acid Sequence↗
PubMed1992

Use of suppressor analysis to identify DNA polymerase mutations in herpes simplex virus which affect deoxynucleoside triphosphate substrate specificity.

Herpes simplex virus DNA polymerase mutations which map in the N-terminal part of the protein and appear to alter deoxynucleoside triphosphate (dNTP) substrate specificity are described. These mutations suppress a drug hypersensitivity associated with the downstream mutation, Aphr10. We suggest that the mutant residues form part of the dNTP-binding site, a site previously thought to be confined to the C terminus.

Aphidicolin↗
PubMed1984

Phospholipid substrate-specificity of the L-serine base-exchange enzyme in rat liver microsomal fraction.

The specificity of the L-serine base-exchange enzyme towards the fatty acid composition of the phospholipid substrate was investigated with a rat liver microsomal fraction. The relative rates of L-serine incorporation into saturated-hexaenoic, saturated-pentaenoic, saturated-tetraenoic, saturated-trienoic, dienoic-dienoic, monoenoic-dienoic, saturated-dienoic and saturated-monoenoic + saturated-saturated phosphatidylserine molecular species were 42, 5, 23, 4, 5, 4, 5 and 11% respectively. This is similar to, but not identical with, the relative mass abundance of these molecular species in total liver cell phosphatidylserines. The results indicate that the substrate-specificity of the L-serine base-exchange enzyme can at least in part explain the observed fatty acid composition of rat liver phosphatidylserines.

Animals↗
PubMed1996

Restriction of substrate specificity of subtilisin E by introduction of a side chain into a conserved glycine residue.

Substitution of the conserved Gly127 for residues having a side chain markedly changed the substrate specificity of subtilisin E from Bacillus subtilis. The crystallographic findings suggested that Gly127 is responsible for accepting even the large P1 substrates, and the marked change of specificity was attributed to the introduction of a side chain in this position. To test this hypothesis, Gly127 was replaced with 3 non-charged amino acids, Ala, Ser and Val. When assayed with synthetic peptide substrates, all mutants purified from the periplasmic space in Escherichia coli showed a marked preference for small P1 substrate up to 150-fold relative to the wild-type. The kinetic data and molecular modeling analysis suggest that large hydrophobic P1 residues were unable to access the binding pocket due to steric hindrance.

Amino Acid Sequence↗
PubMed1981

Physicochemical property modification strategies based on enzyme substrate specificities I: rationale, synthesis, and pharmaceutical properties of aspirin derivatives.

A rationale is developed for drug physicochemical property modification based on making derivatives that are substrates for known enzymes. The approach requires knowledge of the enzyme-substrate specificities to select the appropriate derivative. As a class, the digestive enzymes represent possible reconversion sites. It is shown that by using only known specificities of these enzymes, the physicochemical properties of a drug may be modified in almost any manner desired by appropriate derivative choice, with enzymatic regeneration remaining effective. The strategy is applied to making a stable aspirin derivative that is activated in vivo. Of the derivatives made, aspirin phenylalanine ethyl ester was shown to be stable in suspension form for over 4 years. It was also shown that aspirin is regenerated form the derivative in the presence of the enzymes alpha-chymotrypsin and carboxypeptidase in vitro. This biochemical approach to drug physicochemical property modification offers a new and powerful rationale for improving drug product efficacy.

Amines↗
PubMed1993

The acceptor substrate specificity of porcine submaxillary UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase is dependent on the amino acid sequences adjacent to serine and threonine residues.

The acceptor substrate specificity of a pure polypeptide N-acetylgalactosaminyltransferase has been examined with synthetic polypeptides with sequences identical, or similar to those found in porcine mucin or human erythropoietin. The sequences adjacent to either threonine or serine markedly influence the formation of GalNAc-O-Thr and GalNAc-O-Ser. Examination of the mucin-like peptide VLGXXAV, where X is Thr, Ser, or Ala, shows only Thr-containing peptides to be acceptors. The best substrate is formed when XX is TT. Peptides with XX as either AT or TA are less effective and those with XX as either ST or TS are much less effective acceptors. The amino acids adjacent to serine in the peptide formed by residues 121-131 in human erythropoietin, PPDAASAAPLR, also markedly influence the formation of GalNAc-O-Ser. Thus, PPDASSSAPLR and PPDVVSVVPLR are about 5- and 30-fold, respectively, less active than the erythropoietin peptide. The peptide PPDGGSGGPLR is inactive. The shorter peptide DAASAAPL is also about 5-fold less active than the full-length peptide, but the peptide AASAA is inactive. These studies indicate that one transferase can form both GalNAc-O-Ser and GalNAc-O-Thr residues when the sequences adjacent to the glycosylated residue are of the proper kind. Thus, in contrast to earlier suggestions, there is no evidence that different transferases form GalNAc-O-Ser and GalNAc-O-Thr. Examination of tissue homogenates from various tissues confirms this conclusion.

Amino Acid Sequence↗
PubMed2001

Alteration of the substrate specificity of a modular polyketide synthase acyltransferase domain through site-specific mutations.

Cassette replacement of acyltransferase (AT) domains in 6-deoxyerythronolide B synthase (DEBS) with heterologous AT domains with different substrate specificities usually yields the predicted polyketide analogues. As reported here, however, several AT replacements in module 4 of DEBS failed to produce detectable polyketide under standard conditions, suggesting that module 4 is sensitive to perturbation of the protein structure when the AT is replaced. Alignments between different modular polyketide synthase AT domains and the Escherichia coli fatty acid synthase transacylase crystal structure were used to select motifs within the AT domain of module 4 to re-engineer its substrate selectivity and minimize potential alterations to protein folding. Three distinct primary regions of AT4 believed to confer specificity for methylmalonyl-CoA were mutated into the sequence seen in malonyl-CoA-specific domains. Each individual mutation as well as the three in combination resulted in functional DEBSs that produced mixtures of the natural polyketide, 6-deoxyerythronolide B, and the desired novel analogue, 6-desmethyl-6-deoxyerythronolide B. Production of the latter compound indicates that the identified sequence motifs do contribute to AT specificity and that DEBS can process a polyketide chain incorporating a malonate unit at module 4. This is the first example in which the extender unit specificity of a PKS module has been altered by site-specific mutation and provides a useful alternate method for engineering AT specificity in the combinatorial biosynthesis of polyketides.

Acyltransferases↗
PubMed2004

P-glycoprotein is a factor in the uptake of dextromethorphan, but not of melperone, into the mouse brain: evidence for an overlap in substrate specificity between P-gp and CYP2D6.

In this study, the role of P-glycoprotein (P-gp) for the pharmacokinetics of dextromethorphan, a CYP2D6 substrate, and of melperone, a CYP2D6 inhibitor, was investigated. The substances were administered subcutaneously near the nape of the neck of wild-type mice and of abcb1ab (-/-) mice. One hour after injection, concentrations of the two drugs in cerebrum, plasma and in different organs were measured by high-performance liquid chromatography. No significant differences between wild-type mice and abcb1ab (-/-) mice were observed for melperone, suggesting that P-gp is not involved in the uptake of melperone into the brain or other organs of mice. The concentration of dextromethorphan in the brain was more than twice as high in abcb1ab (-/-) mice compared to wild-type mice. Therefore, P-gp appears to be a factor in the uptake of dextromethorphan into the mouse brain, and abcb1-polymorphisms need to be considered for CYP2D6 phenotyping experiments with this drug. There is an overlap in substrate specificity between P-gp and CYP2D6. P-gp is a factor in the uptake of dextromethorphan, but not of melperone.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1994

Substrate specificity of L-delta-(alpha-aminoadipoyl)-L-cysteinyl-D-valine synthetase from Cephalosporium acremonium: demonstration of the structure of several unnatural tripeptide products.

Potential substrates for L-delta-(alpha-aminoadipoyl)-L-(cysteinyl)-D-valine (ACV) synthetase were initially identified using both the amino-acid-dependent ATP<-->pyrophosphate exchange reaction catalysed by the enzyme and the incorporation of 14C-radiolabelled cysteine and valine into potential peptide products. S-Carboxymethylcysteine was an effective substitute for alpha-aminoadipate and both allylglycine and vinylglycine could substitute for cysteine, indicating that the thiol group of cysteine is not essential for peptide formation. L-allo-Isoleucine but not L-isoleucine substituted effectively for valine. The structures of the presumed peptide products derived from these amino acids were confirmed by combined use of electrospray-ionization m.s. (e.s.m.s.) and 1H n.m.r. These results clearly indicate that, in common with other peptide synthetases, but in contrast with ribosomal peptide synthesis, ACV synthetase has a relatively broad substrate specificity.

2-Aminoadipic Acid↗
PubMed1988

Substrate specificities of 5'-deoxy-5'-methylthioadenosine phosphorylase from Trypanosoma brucei brucei and mammalian cells.

The separation by chromatofocusing of two distinct purine nucleoside cleaving activities from crude extracts of Trypanosoma brucei brucei is described. One catalyzes the reversible phosphorolysis of 5'-deoxy-5'-methylthioadenosine (MeSAdo) and adenosine (Ado) and was designated an MeSAdo/Ado phosphorylase, while the other catalyzes the hydrolysis of adenosine, inosine, and guanosine but not MeSAdo. The substrate specificity of trypanosomal MeSAdo/Ado phosphorylase differed from that of a mammalian MeSAdo phosphorylase (derived from murine Sarcoma 180 cells) in that it was able to phosphorolyze 2'-deoxyadenosine, 3'-deoxyadenosine and 2',3'-dideoxyadenosine. In addition, the trypanosomal phosphorylase was able to utilize the nucleoside analog, 6-methylpurine 2'-deoxyribonucleoside, as an alternative substrate, whereas the mammalian enzyme could not. Because of these differences, cytotoxic analogs of MeSAdo may be designed that are selectively activated by the trypanosomal MeSAdo/Ado phosphorylase.

Adenosine↗