Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:3.4.24.27 (thermolysin)
1,894 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Escherichia coli peptide deformylase, a member of the zinc metalloproteases family, is made up of an active core domain composed of 147 residues and of an additional and dispensable C-terminal tail of 21 residues. The three-dimensional structure of the catalytic core could be studied by NMR. 1H and 15N NMR resonances assignments were obtained by two-dimensional and three-dimensional heteronuclear spectroscopy. The structure could be calculated using a set of 1015 restraints for the 147 residues of the enzyme. The overall structure is composed of a series of antiparallel beta-strands which surround two perpendicular alpha-helices. The C-terminal helix contains the HEXXH motif, which is crucial for activity. This helical arrangement and the way the histidines bind the zinc ion clearly are structurally reminiscent of the other members of the metalloprotease family, such as thermolysin or metzincins. Nevertheless, the overall arrangement of secondary and tertiary structures of peptide deformylase and the positioning of its third zinc ligand (a cysteine) are quite different from those of the other members of the family. These discrepancies, together with several biochemical differences, lead us to propose that peptide deformylase is the first example of a new class of the zinc-metalloproteases family. Studies of the interaction of peptide deformylase with either an inhibitor of the reaction or a product of the catalysed reaction, Met-Ala-Ser, as well as comparisons with the structures of other enzymes of the family, have enabled us to delineate the area corresponding to their binding site. The structural basis of the specificity of recognition of the formyl group is discussed in the context of the protease superfamily.
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PMID:A new subclass of the zinc metalloproteases superfamily revealed by the solution structure of peptide deformylase. 884 3

To probe proximity relationships between different amino acids in the interhelical loops in the cytoplasmic domain of rhodopsin, we are using a general approach in which two cysteine residues are introduced at different locations. Here we report on the characteristics of one such mutant that contains the naturally occurring cysteine 316 near the cytoplasmic end of helix G and a second cysteine at position 65 (H65C), near the cytoplasmic end of helix A. The mutant protein after expression in COS-1 cells and reconstitution with 11-cis-retinal can be bound to anti-rhodopsin antibody 1D4-Sepharose at pH 6 in a form that contains the two cysteines in the free sulfhydryl form. In this form, the mutant protein reacts as expected with N-ethylmaleimide in the dark at room temperature and can be derivatized with nitroxide spin labels. However, under appropriate conditions, the mutant can be isolated with the cysteines in the disulfide form, which has been characterized by analysis of fragments produced on proteolysis with thermolysin. A study of the interactions between nitroxide spin labels attached to the two cysteine residues in the mutant protein indicates that in the dark state they are within about 10 A of each other. On illumination the distance between the spin labels increases. Collectively, the above results show that, upon folding of the mutant opsin in vivo, cysteines 65 and 316, and by inference, helices A and G, are in proximal locations and move further apart upon photoactivation.
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PMID:Structure and function in rhodopsin. Cysteines 65 and 316 are in proximity in a rhodopsin mutant as indicated by disulfide formation and interactions between attached spin labels. 891 88

Monobromobimane (mBBr) is a substrate of both mu- and alpha-class rat liver glutathione S-transferases, with Km values of 0.63 microM and 4.9 microM for the mu-class isozymes 3-3 and 4-4, respectively, and 26 microM for the alpha-class isozymes 1-1 and 2-2. In the absence of substrate glutathione, mBBr acts as an affinity label of the 1-1 as well as mu-class isozymes, but not of the alpha-class 2-2 isozyme. Incubation of rat liver isozyme 1-1 with mBBr at pH 7.5 and 25 degrees C results in a time-dependent inactivation of the enzyme but at a slower (threefold) rate than for reactions with the mu-class isozyme 3-3 and 4-4. The rate of inactivation of 1-1 isozyme by mBBr is not decreased but, rather, is slightly enhanced by S-methyl glutathione. In contrast, 17 beta-estradiol-3,17-disulfate (500 microM) gives a 12.5-fold decrease in the observed rate constant of inactivation by 4 mM mBBr. When incubated for 60 min with 4 mM mBBr, the 1-1 isozyme loses 60% of its activity and incorporates 1.7 mol reagent/mol subunit. Peptide analysis after thermolysin digestion indicates that mBBr modification is equally distributed between two cysteine residues at positions 17 and 111. Modification at these two sites is reduced equally in the presence of the added protectant, 17 beta-estradiol-3,17-disulfate, suggesting that Cys 17 and Cys 111 reside within or near the enzyme's steroid binding sites. In contrast to the 1-1 isozyme, the other alpha-class isozyme (2-2) is not inactivated by mBBr at concentrations as high as 15 mM. The different reaction kinetics and modification sites by mBBr suggest that distinct binding site structures are responsible for the characteristic substrate specificities of glutathione S-transferase isozymes.
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PMID:Probing the active site of alpha-class rat liver glutathione S-transferases using affinity labeling by monobromobimane. 900 75

The sites of the disulfide bonds in a napin protein isolated from Brassica napus have been identified by proteolytic cleavage and subsequent peptide mapping by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). Napins consist of two polypeptide chains containing two and six cysteine residues, respectively, that are held together by disulfide bonds. Upon initial cleavage of native napin by Endo-Lys-C, a disulfide-linked core complex of four peptides was obtained. This core peptide was isolated by reversed-phase HPLC and further digested by thermolysin, and the resulting fragments were identified by MALDI-MS. In a separate set of experiments, intact napin was subjected to proteolysis by thermolysin, and an isolated disulfide-linked peptide of interest was subdigested again using thermolysin. The combined data resulting from these experiments allowed the assignment of the disulfide linkages in a relatively abundant napin isoform, BngNAP1, apart from an ambiguity concerning the adjacent cysteines at positions 14' and 15' of the long chain. Two intermolecular disulfide bonds link Cys10 (short chain) with Cys25' (long chain) and Cys23 with Cys14' (or Cys15'), respectively. The long chain of napin contains two intramolecular disulfide bonds connecting Cys27' with Cys80' and Cys14' (or Cys15') with Cys72'.
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PMID:Assignment of the disulfide bonds in napin, a seed storage protein from Brassica napus, using matrix-assisted laser desorption ionization mass spectrometry. 904 25

The thermal inactivation of broad specificity proteases such as thermolysin and subtilisin is initiated by partial unfolding processes that render the enzyme susceptible to autolysis. Previous studies have revealed that a surface-located region in the N-terminal domain of the thermolysin-like protease produced by Bacillus stearothermophilus is crucial for thermal stability. In this region a disulfide bridge between residues 8 and 60 was designed by molecular modelling, and the corresponding single and double cysteine mutants were constructed. The disulfide bridge was spontaneously formed in vivo and resulted in a drastic stabilization of the enzyme. This stabilization presents one of the very few examples of successful stabilization of a broad specificity protease by a designed disulfide bond. We propose that the success of the present stabilization strategy is the result of the localization and mutation of an area of the molecule involved in the partial unfolding processes that determine thermal stability.
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PMID:Extreme stabilization of a thermolysin-like protease by an engineered disulfide bond. 911 Oct 13

Endopeptidase EC 3.4.24.15 (EP24.15) is a thermolysin-like metalloendopeptidase involved in the regulated metabolism of a number of neuropeptides. Unlike other thermolysin-like peptidases EP24.15 displays a unique thiol activation, a mechanism that is not clearly understood. In this study we show that both recombinant and tissue-derived EP24.15 are activated up to 8-fold by low concentrations (0.1 mM) of dithiothreitol. Additionally, under non-reducing conditions, recombinant and native EP24.15 forms multimers that can be returned to the monomeric form by reduction. We have also shown that competitive inhibitor binding occurs only to the monomeric form, which indicates that catalytic site access is restricted in the multimeric forms. Through systematic site-directed mutagenesis we have identified that cysteine residues 246, 253, and possibly 248 are involved in the formation of these multimers. Furthermore, both a double mutant (C246S/C253S) and a triple mutant (C246S/C248S/C253S) are fully active in the absence of reducing agents, as measured by both inhibitor binding and hydrolysis. The formation and disruption of disulfide bonds involving these cysteine residues may be a mechanism by which EP24.15 activity is regulated through changes in intra- and extracellular redox potential.
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PMID:Thiol activation of endopeptidase EC 3.4.24.15. A novel mechanism for the regulation of catalytic activity. 921 80

We determined the cysteine connectivity of protegrin PG-2, a leukocyte-derived antimicrobial peptide, by performing sequential enzyme digestions with chymotrypsin and thermolysin, and monitoring each digest by direct liquid chromatography-electrospray mass spectrometric analysis. This approach resolved the disulphide pairing pattern unambiguously with only picomolar amounts of PG-2. The inferred cysteine connectivity was confirmed by traditional amino acid composition analyses using nanomolar amounts of the protegrin. The results suggest that protegrins will assume a tachyplesin-like, disulphide-stabilized anti-parallel beta-sheet configuration in solution.
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PMID:Determination of disulphide bridges in PG-2, an antimicrobial peptide from porcine leukocytes. 922 98

VanX, one of the five proteins required for the vancomycin-resistant phenotype in clinically pathogenic Enterococci, is a zinc-containing d-Ala-d-Ala dipeptidase. To identify potential zinc ligands and begin defining the active site residues, we have mutated the 2 cysteine, 5 histidine, and 4 of the 28 aspartate and glutamate residues in the 202 residue VanX protein. Of 10 mutations, 3 cause inactivation and greater than 90% loss of zinc in purified enzyme samples, implicating His116, Asp123, and His184 as zinc-coordinating residues. Homology searches using the 10 amino acid sequence SxHxxGxAxD, in which histidine and aspartate residues are putative zinc ligands, identified the metal coordinating ligands in the N-terminal domain of the murine Sonic hedgehog protein, which also exhibits an architecture for metal coordination identical to that observed in thermolysin from Bacillus thermoproteolyticus. Furthermore, this 10 amino acid consensus sequence is found in the Streptomyces albus G zinc-dependent N-acyl-d-Ala-d-Ala carboxypeptidase, an enzyme catalyzing essentially the same d-Ala-d-Ala dipeptide bond cleavage as VanX, suggesting equivalent mechanisms and zinc catalytic site architectures. VanX residue Glu181 is analogous to the Glu143 catalytic base in B. thermoproteolyticus thermolysin, and the E181A VanX mutant has no detectable dipeptidase activity, yet maintains near-stoichiometric zinc content, a result consistent with the participation of the residue as a catalytic base.
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PMID:Mutational analysis of potential zinc-binding residues in the active site of the enterococcal D-Ala-D-Ala dipeptidase VanX. 926 30

Nitrile hydratase (NHase) from Rhodococcus sp. N-771 is a photoreactive enzyme that is inactivated by nitrosylation of the non-heme iron center and activated by photodissociation of nitric oxide (NO). To obtain structural information on the iron center, we isolated peptide complexes containing the iron center by proteolysis. When the tryptic digest of the alpha subunit isolated from the inactive form was analyzed by reversed-phase high performance liquid chromatography, the absorbance characteristic of the nitrosylated iron center was observed in the peptide fragment, Asn105-Val-Ile-Val-Cys-Ser-Leu-Cys-Ser-Cys-Thr-Ala-Trp-Pro-Ile-Leu - Gly-Leu-Pro-Pro-Thr-Trp-Tyr-Lys128. The peptide contained 0.79 mol of iron/mol of molecule as well as endogenous NO. Subsequently, by digesting the peptide with thermolysin, carboxypeptidase Y, and leucine aminopeptidase M, we found that the minimum peptide segment required for the nitrosylated iron center is the 11 amino acid residues from alphaIle107 to alphaTrp117. Furthermore, by using mass spectrometry, protein sequence, and amino acid composition analyses, we have shown that the 112th Cys residue of the alpha subunit is post-translationally oxidized to a cysteine-sulfinic acid (Cys-SO2H) in the NHase. These results indicate that the NHase from Rhodococcus sp. N-771 has a novel non-heme iron enzyme containing a cysteine-sulfinic acid in the iron center. Possible ligand residues of the iron center are discussed.
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PMID:Structure of the photoreactive iron center of the nitrile hydratase from Rhodococcus sp. N-771. Evidence of a novel post-translational modification in the cysteine ligand. 936 4

Protein synthesis in bacteria involves the formylation and deformylation of the N-terminal methionine. As eukaryotic organisms differ in their protein biosynthetic mechanisms, peptide deformylase, the bacterial enzyme responsible for deformylation, represents a potential target for antibiotic studies. Here we report the crystallization and 2.9 A X-ray structure solution of the zinc containing Escherichia coli peptide deformylase. While the primary sequence, tertiary structure, and use of coordinated cysteine suggest that E. coli deformylase belongs to a new subfamily of metalloproteases, the environment around the metal appears to have strong geometric similarity to the active sites of the thermolysin family. This suggests a possible similarity in their hydrolytic mechanisms. Another important issue is the origin of the enzyme's specificity for N-formylated over N-acetylated substrates. Based on the structure, the specificity appears to result from hydrogen-bonding interactions which orient the substrate for cleavage, and steric factors which physically limit the size of the N-terminal carbonyl group.
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PMID:Crystal structure of the Escherichia coli peptide deformylase. 937 69


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