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C T Walsh

Publications and source records attributed to C T Walsh.

At least 109 records · Page 6Linked to original sources
PubMed1997

Divalent ion effects and insights into the catalytic mechanism of protein tyrosine kinase Csk.

Csk (C-terminal Src kinase) is a protein tyrosine kinase which catalyzes the transfer of the gamma-phosphoryl group of ATP to the tyrosine hydroxyl of proteins in the presence of a divalent ion. Previous work with poly(Glu,Tyr) as the tyrosine-containing substrate and Mn as the divalent ion defined a ternary complex mechanism with ADP product release partially rate-determining [Cole, P. A., et al. (1994) J. Biol, Chem. 269, 30880-30887]. In this current study, ionic strength and divalent ion effects were probed. Increasing ionic strength led to a dramatic rise in the poly(Glu,Tyr) [4:l poly(glutamate:tyrosine)] K(m) and had little effect on the ATP K(m) or Kcat in Csk-mediated phosphoryl transfer. This finding allowed the dead-end peptide inhibitor EDNEFTA to be characterized as a linear competitive inhibitor of poly(Glu,Tyr) and a linear noncompetitive inhibitor of ATP. Taken together with previous data, the overall kinetic mechanism could now be assigned as random substrate binding, ternary complex. Compared to Mn, Mg was shown to sustain phosphoryl transfer with a 2.5-fold higher Kcat but K(m)'s for ATP and poly(Glu,Tyr) that were some 15-20-fold higher. An elevated ADP Ki and microviscosity effects were most suggestive of a kinetic mechanism with fast ADP release, and the chemical step fully rate-determining in the Mg-dependent reaction. Steady-state kinetic analyses of Csk reactions with Co and Ni in addition to Mg and Mn on wild-type and D314E Csk with ATP and ATP gamma S [adenosine 5'-O-(3-thiotriphosphate)] as substrates were performed. The Kcat thio effects [Kcat(ATP)/Kcat(ATP gamma S)] were inversely correlated with metal thiophilicity in both wild-type and D314E mutant Csk reactions, although the relationship was less pronounced in the latter. These results appear to underscore the role of gamma-phosphoryl hydrogen bonding/salt bridging in the wild-type Csk reaction transition state, which is somewhat perturbed in the D314E Csk reaction. In the case of the Ni reaction, the Kcat thio effect was reduced to about 2 in the wild-type and D314E mutant Csk reactions. Relevance with regard to the degree of nucleophilic attack in the transition state, i.e., associative vs dissociative character of phosphoryl transfer, is discussed.

Aspartic Acid↗
PubMed1997

Kinetic characterization of wild-type and S229A mutant MurB: evidence for the role of Ser 229 as a general acid.

X-ray derived structural data predicted that serine 229 was positioned to act as a proton donor to the developing C2 carbanion during the reduction of enolpyruvyl-UDP-N-acetylglucosamine catalyzed by the bacterial peptidoglycan biosynthetic flavoenzyme MurB. To investigate this effect, a mutant where serine 229 was replaced by alanine was constructed and purified. Kinetic analysis of the two half-reactions for the mutant enzyme revealed a 9-fold decrease in the reduction of EFlox by NADPH and a dramatic 10(7)-fold decrease in the reoxidation of EFlred with the enolpyruvyl substrate. In addition, studies of S229A with the substrate analog, (E)-enolbutyryl-UDP-N-acetylglucosamine, showed a striking bias of the partitioning toward formation of the (Z) geometric isomer as opposed to formation of the reduced product UDP-methylmuramic acid, which was the predominant product in wild-type MurB. These studies provide evidence for the proposed role of this active-site serine as a general acid catalyst.

Base Sequence↗
PubMed1997

X-ray crystal structures of the S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine at 1.8-A resolution.

MurB catalyzes the second committed step in the synthesis of peptidoglycan, a key component of the bacterial cell wall. The crystal structures of both a S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine were solved and refined at 1.8 A resolution. The single point mutation of residue 229 from serine to alanine eliminated a hydroxyl group which has previously been proposed to play a critical role as a proton donor during the second half-reaction of MurB, namely, reoxidation of FADH2 and reduction of the enolpyruvyl substrate. The mutation also resulted in the loss of the water molecule-hydrogen bonded to the serine hydroxyl in the wild-type structure changing the hydrogen-bonding network with in the active site. Comparison of the wild-type and S229A mutant structures confirms that the dramatic kinetic defect of an approximately 10(7)-fold decrease observed for the Ser 229 Ala mutant in the second half-reaction [Benson, T.E., Walsh, C.T., & Massey, V. (1997) Biochemistry 36, 796-805] is a direct result of the loss of the serine hydroxyl moiety rather than other nonspecific active-site changes or general structural defects.

Binding Sites↗
PubMed1997

Dissection of glutathionylspermidine synthetase/amidase from Escherichia coli into autonomously folding and functional synthetase and amidase domains.

The bifunctional glutathionylspermidine synthetase/amidase from Escherichia coli catalyzes both the ATP-dependent formation of an amide bond between N1 of spermidine (N-(3-amino)propyl-1, 4-diaminobutane) and the glycine carboxylate of glutathione (gamma-Glu-Cys-Gly) and the opposing hydrolysis of this amide bond (Bollinger, J. M., Jr., Kwon, D. S., Huisman, G. W., Kolter, R., and Walsh, C. T. (1995) J. Biol. Chem. 270, 14031-14041). In our previous work describing its initial characterization, we proposed that the 619-amino acid (70 kDa) protein might possess separate amidase (N-terminal) and synthetase (C-terminal) domains. In the present study, we have confirmed this hypothesis by expression of independently folding and functional amidase and synthetase modules. A fragment containing the C-terminal 431 amino acids (50 kDa) has synthetase activity only, with steady-state kinetic parameters similar to the full-length protein. A fragment containing the N-terminal 225 amino acids (25 kDa) has amidase activity only and is significantly activated relative to the full-length protein for hydrolysis of glutathionylspermidine analogs. This observation suggests that the amidase activity in the full-length protein is negatively autoregulated. The amidase active site catalyzes hydrolysis of amide and ester derivatives of glutathione (e.g. glutathione ethyl ester and glutathione amide) but lacks activity toward acetylspermidine (N1 and N8) and acetylspermine (N1), indicating that glutathione provides the primary recognition determinants for glutathionylspermidine amide bond cleavage. No metal ion is required for the amidase activity. A tetrahedral phosphonate analogue of glutathionylspermidine, designed as a mimic of the proposed tetrahedral intermediate for either reaction, inhibits the synthetase activity (Ki approximately 10 microM) but does not inhibit the amidase activity.

Amide Synthases↗
PubMed1997

Aldehyde and phosphinate analogs of glutathione and glutathionylspermidine: potent, selective binding inhibitors of the E. coli bifunctional glutathionylspermidine synthetase/amidase.

INTRODUCTION: The tripeptide glutathione is converted to glutathionylspermidine (Gsp) in Escherichia coli and in trypanosomatid parasites by an ATP-cleaving Gsp synthetase activity. In parasites, an additional glutathionylation forms bis-(glutathionyl)-spermidine, trypanothione, believed to be the major surveillance thiol involved in oxidant defense mechanisms in trypanosomatid parasites. In E. coli, the Gsp synthetase is part of a bifunctional enzyme opposed by the hydrolytic Gsp amidase. RESULTS: Gsp amidase and Gsp synthetase activities of the bifunctional E. coli enzyme can be separately targeted by potent, selective slow-binding inhibitors that induce time-dependent inhibition. The inhibitor gamma-Glu-Ala-Gly.CHO most probably captures Cys59 and accumulates as the tetrahedral adduct in the amidase active site. Inhibitory Gsp phosphinate analogs are phosphorylated by ATP to yield phosphinophosphate analogs in the synthetase active site. Binding of phosphinophosphate in the Gsp synthetase active site potentiates the inhibition affinity for the aldehyde at the Gsp amidase active site by two orders of magnitude. CONCLUSIONS: Time-dependent inhibition of the Gsp amidase activity by the aldehyde substrate analog supports previous work that suggests glutathionyl acyl-enzyme intermediate formation in the Gsp amidase reaction mechanism. Use of potent selective inhibitors against Gsp amidase (aldehyde) and Gsp synthetase (phosphinate) activities provides further evidence of interdomain communication in the bifunctional enzyme from E. coli.

Aldehydes↗
PubMed1997

Ability of Streptomyces spp. acyl carrier proteins and coenzyme A analogs to serve as substrates in vitro for E. coli holo-ACP synthase.

INTRODUCTION: The polyketide natural products are assembled by a series of decarboxylation/condensation reactions of simple carboxylic acids catalyzed by polyketide synthase (PKS) complexes. The growing chain is assembled on acyl carrier protein (ACP), an essential component of the PKS. ACP requires posttranslational modification on a conserved serine residue by covalent attachment of a 4'-phosphopantetheine (P-pant) cofactor to yield active holo-ACP. When ACPs of Streptomyces type II aromatic PKS are overproduced in E. coli, however, typically little or no active holo-ACP is produced, and the ACP remains in the inactive apo-form. RESULTS: We demonstrate that E. coli holo-ACP synthase (ACPS), a fatty acid biosynthesis enzyme, can catalyze P-pant transfer in vitro to the Streptomyces PKS ACPs required for the biosynthesis of the polyketide antibiotics granaticin, frenolicin, oxytetracycline and tetracenomycin. The catalytic efficiency of this P-pant transfer reaction correlates with the overall negative charge of the ACP substrate. Several coenzyme A analogs, modified in the P-pant portion of the molecule, are likewise able to serve as substrates in vitro for ACPS. CONCLUSIONS: E coli ACPS can serve as a useful reagent for the preparation of holo-forms of Streptomyces ACPs as well as holo-ACPs with altered phosphopantetheine moieties. Such modified ACPs should prove useful for studying the role of particular ACPs and the phosphopantetheine cofactor in the subsequent reactions of polyketide and fatty acid biosynthesis.

Acyl Carrier Protein↗
PubMed1997

Post-translational modification of polyketide and nonribosomal peptide synthases.

The past year has witnessed a major advance in the study of polyketide and nonribosomal peptide biosynthesis with the identification of the phosphopantetheinyl transferase enzyme family, enzymes required to produce active, post-translationally modified polyketide and peptide synthases. Phosphopantetheinyl transferases required for fatty acid, peptide and siderophore biosynthesis have been characterized and a consensus sequence noted in order to facilitate future identification of additional proteins catalyzing phosphopantetheinyl transfer.

Fatty Acids↗
PubMed1997

The leader peptide is essential for the post-translational modification of the DNA-gyrase inhibitor microcin B17.

Microcin B17 (MccB17) is a ribosomally encoded DNA-gyrase inhibitor. Ribosomally encoded antibiotics are derived from precursors containing an N-terminal leader, which is removed during maturation, and a C-terminal structural peptide. PreMccB17, the translational product of mcbA, is modified into proMccB17 by the action of three enzymes, McbB, McbC, and McbD. A chromosomally encoded peptidase then converts proMccB17 into MccB17. The role of McbB, McbC, and McbD is to convert glycine, cysteine, and serine residues present in preMccB17 into four thiazole and four oxazole rings. Using a modification-specific antibody rather than antimicrobial activity, we show that the 26-amino-acid N-terminal leader of preMccB17 is essential for the conversion of preMccB17 into proMccB17. Neither a preMccB17 peptide lacking the leader nor a preMccB17-beta-galactosidase fusion lacking the leader are post-translationally modified.

Bacteriocins↗
PubMed1997

Transcriptional regulation of the Enterococcus faecium BM4147 vancomycin resistance gene cluster by the VanS-VanR two-component regulatory system in Escherichia coli K-12.

An Escherichia coli K-12 model system was developed for studying the VanS-VanR two-component regulatory system required for high-level inducible vancomycin resistance in Enterococcus faecium BM4147. Our model system is based on the use of reporter strains with lacZ transcriptional and translational fusions to the PvanR or PvanH promoter of the vanRSHAX gene cluster. These strains also express vanR and vanS behind the native PvanR promoter, the arabinose-inducible ParaB promoter, or the rhamnose-inducible PrhaB promoter. Our reporter strains have the respective fusions stably recombined onto the chromosome in single copy, thereby avoiding aberrant regulatory effects that may occur with plasmid-bearing strains. They were constructed by using allele replacement methods or a conditionally replicative attP plasmid. Using these reporter strains, we demonstrated that (i) the response regulator VanR activates PvanH, but not PvanR, expression upon activation (phosphorylation) by the partner kinase VanS, the noncognate kinase PhoR, or acetyl phosphate, indicating that phospho-VanR (P-VanR) is a transcriptional activator; (ii) VanS interferes with activation of VanR by PhoR or acetyl phosphate, indicating that VanS also acts as a P-VanR phosphatase; and (iii) the conserved, phosphate-accepting histidine (H164) of VanS is required for activation (phosphorylation) of VanR but not for deactivation (dephosphorylation) of P-VanR. Similar reporter strains may be useful in new studies on these and other interactions of the VanS-VanR system (and other systems), screening for inhibitors of these interactions, and deciphering the molecular logic of the signal(s) responsible for activation of the VanS-VanR system in vivo. Advantages of using an E. coli model system for in vivo studies on VanS and VanR are also discussed.

Bacterial Proteins↗
PubMed1997

Active-site residues of cyclophilin A are crucial for its incorporation into human immunodeficiency virus type 1 virions.

Human immunodeficiency virus type 1 (HIV-1) incorporates the cellular peptidyl-prolyl cis-trans isomerase cyclophilin A (CyPA), the cytosolic receptor for the immunosuppressant cyclosporin A (CsA). CsA inhibits the incorporation of CyPA and reduces HIV-1 virion infectivity but is inactive against closely related primate lentiviruses that do not interact with CyPA. The incorporation of CyPA into HIV-1 virions is mediated by a specific interaction with a proline-containing, solvent-exposed loop in the capsid (CA) domain of the Gag polyprotein. CsA, which disrupts the interaction with CA, binds at the active site of CyPA. To test whether active-site residues are also involved in the interaction with HIV-1 CA, we used a panel of previously characterized active-site mutants of human CyPA. Expression vectors for epitope-tagged wild-type and mutant CyPA were transfected into COS-gamma cells along with HIV-1 proviral DNA, and the virions produced were analyzed for the presence of tagged proteins. Cotransfection of the wild-type expression vector led to the incorporation of readily detectable amounts of epitope-tagged CyPA into HIV-1 virions. One CyPA mutant with a substantially decreased sensitivity to CsA was incorporated with wild-type efficiency, demonstrating that the requirements for binding to CsA and to HIV-1 CA are not identical. The remaining six CyPA mutants were incorporated with markedly reduced efficiency, providing in vivo evidence that HIV-1 CA interacts with the active site of CyPA.

Amino Acid Isomerases↗
PubMed1996

Competitive inhibition of calcineurin phosphatase activity by its autoinhibitory domain.

Calcineurin (protein phosphatase 2B), a calmodulin- and calcium-dependent serine/threonine phosphatase, appears to be regulated by a C-terminal autoinhibitory domain. A 25 amino acid peptide derived from this domain inhibits calcineurin phosphatase activity in vitro. Here we show that a 97 amino acid fragment of the calcineurin A alpha C-terminus is approx. 8-fold more potent than the shorter peptide in calcineurin inhibition experiments. Mutation of an evolutionarily conserved Asp to Asn, previously shown to disrupt calcium-dependent signalling and calcineurin regulation in T-lymphocytes, greatly reduced inhibition by the autoinhibitory domain in vitro. Kinetic analysis of wild-type and mutated autoinhibitory domains show that both are competitive inhibitors of calcineurin phosphatase activity with Ki values of 5.0 +/- 0.2 microM and 36.0 +/- 3.7 microM respectively. This suggests intrasteric regulation of calcineurin, with the autoinhibitory domains interacting at the active site of the enzyme. The competitive behaviour of the autoinhibitory domains contrasts with the mechanism of calcineurin inhibition by immunosuppressant-immunophilin complexes, which have been shown to bind to calcineurin at a region removed from the active site.

Allosteric Regulation↗
PubMed1996

Altered recognition mutants of the response regulator PhoB: a new genetic strategy for studying protein-protein interactions.

Two-component regulatory systems require highly specific interactions between histidine kinase (transmitter) and response regulator (receiver) proteins. We have developed a novel genetic strategy that is based on tightly regulated synthesis of a given protein to identify domains and residues of an interacting protein that are critical for interactions between them. Using a reporter strain synthesizing the nonpartner kinase VanS under tight arabinose control and carrying a promoter-lacZ fusion activated by phospho-PhoB, we isolated altered recognition (AR) mutants of PhoB showing enhanced activation (phosphorylation) by VanS as arabinose-dependent Lac+ mutants. Changes in the PhoBAR mutants cluster in a "patch" near the proposed helix 4 of PhoB based on the CheY crystal structure (a homolog of the PhoB receiver domain) providing further evidence that helix 4 lies in the kinase-regulator interface. Based on the CheY structure, one mutant has an additional change in a region that may propagate a conformational change to helix 4. The overall genetic strategy described here may also be useful for studying interactions of other components of the vancomycin resistance and P1 signal transduction pathways, other two-component regulatory systems, and other interacting proteins. Conditionally replicative oriRR6K gamma attP "genome targeting" suicide plasmids carrying mutagenized phoB coding regions were integrated into the chromosome of a reporter strain to create mutant libraries; plasmids encoding mutant PhoB proteins were subsequently retrieved by P1-Int-Xis cloning. Finally, the use of similar genome targeting plasmids and P1-Int-Xis cloning should be generally useful for constructing genomic libraries from a wide array of organisms.

Bacterial Proteins↗
PubMed1996

From peptide precursors to oxazole and thiazole-containing peptide antibiotics: microcin B17 synthase.

Esherichia coli microcin B17 is a posttranslationally modified peptide that inhibits bacterial DNA gyrase. It contains four oxazole and four thiazole rings and is representative of a broad class of pharmaceutically important natural products with five-membered heterocycles derived from peptide precursors. An in vitro assay was developed to detect heterocycle formation, and an enzyme complex, microcin B17 synthase, was purified and found to contain three proteins, McbB, McbC, and McbD, that convert 14 residues into the eight mono- and bisheterocyclic moieties in vitro that confer antibiotic activity on mature microcin B17. These enzymatic reactions alter the peptide backbone connectivity. The propeptide region of premicrocin is the major recognition determinant for binding and downstream heterocycle formation by microcin B17 synthase. A general pathway for the enzymatic biosynthesis of these heterocycles is formulated.

Adenosine Triphosphate↗
PubMed1996

Gain of D-alanyl-D-lactate or D-lactyl-D-alanine synthetase activities in three active-site mutants of the Escherichia coli D-alanyl-D-alanine ligase B.

Escherichia coli D-Ala-D-Ala ligase (Ddl) and the vancomycin resistance-conferring protein VanA are homologues, but VanA has gained the ability to activate D-lactate (D-Lac) and make the depsipeptide D-Ala-D-Lac as well as D-Ala-D-Ala. This depsipeptide ligase activity of VanA is its crucial catalytic function necessary for phenotypic vancomycin resistance. We report here that three E. coli DdlB active-site mutants that we made previously based on X-ray structure/function predictions have gained interesting new ligase activities. Y216, S150, and E15 form a hydrogen-bonding triad that orients an omega-loop to close over the active site and also to orient substrate D-Ala1. Mutants Y216F and S150A have gained depsipeptide (D-Ala-D-Lac, D-Ala-D-hydroxybutyrate) ligase activity with dipeptide/depsipeptide partition ratios that mimic the pH behavior of VanA. E15Q has negligible depsipeptide synthetase activity but now uniquely activates D-Lac as the electrophilic rather than the nucleophilic partner for condensation with D-Ala to make a regioisomeric D-Lac-D-Ala, an amide rather than an ester product. These results provide insights into the active-site architecture of the ligases and the subsites for recognition of D-Ala VS D-Lac and predict the Y216F substitution will impart D-Ala-D-Lac synthetase activity to Ddls from Grampositive bacteria with intrinsic resistance to vancomycin.

Alanine↗
PubMed1996

Profactor IX propeptide and glutamate substrate binding sites on the vitamin K-dependent carboxylase identified by site-directed mutagenesis.

The vitamin K-dependent carboxylase, a constituent of the endoplasmic reticulum membrane, catalyzes the conversion of reduced vitamin K to vitamin K epoxide and the concomitant conversion of glutamic acid to gamma-carboxyglutamic acid. To study structure-function relationships in the enzyme, seventeen clusters of charged residues of the bovine gamma-glutamyl carboxylase were substituted with alanines using site-specific mutagenesis. Wild-type and mutant carboxylase species were expressed in Chinese hamster ovary cells with an immunodetectable octapeptide inserted at their amino-terminal ends. Out of 17 mutant carboxylase species that contain a total of 41 charged residue to alanine substitutions, K217A/K218A (CBX217/218), R234A/H235A (CBX234/235), R359A/H360A/K361A (CBX359/360/361), R406A/H408A (CBX406/408), and R513A/K515A (CBX513/515) had impaired carboxylase activity compared with the wild-type enzyme. The vitamin K epoxidase activities of these mutants were reduced in parallel with the carboxylase activities. CBX217/218 appears to be inactive. High propeptide concentrations were required for stimulation of carboxylation of FLEEL by CBX234/235, CBX406/408, and CBX513/515, suggesting defects in the propeptide binding site. CBX359/360/361 showed normal affinity for the propeptide, FLEEL, proPT28, and vitamin K hydroquinone but exhibited a low catalytic rate for carboxylation. These results suggest that residue 217, residue 218, or both are either critical for catalysis or for maintaining the structure of a catalytically active enzyme. Regions around residues 234, 406, and 513 define in part the propeptide binding site, while the regions around residue 359 are involved in catalysis.

Amino Acid Sequence↗
PubMed1996

The stress response to ionizing radiation involoves c-Abl-dependent phosphorylation of SHPTP1.

c-Abl is a nonreceptor tyrosine kinase that is activated by certain DNA-damaging agents. The present studies demonstrate that nuclear c-Abl binds constitutively to the protein tyrosine phosphatase SHPTP1. Treatment with ionizing radiation is associated with c-Abl-dependent tyrosine phosphorylation of SHPTP1. The results demonstrate that the SH3 domain of c-Abl interacts with a WPDHGVPSEP motif (residues 417-426) in the catalytic domain of SHPTP1 and that c-Abl phosphorylates C terminal Y536 and Y564 sites. The functional significance of the c-Abl-SHPTP1 interaction is supported by the demonstration that, like c-Abl, SHPTP1 regulates the induction of Jun kinase activity following DNA damage. These findings indicate that SHPTP1 is involved in the response to genotoxic stress through a c-Abl-dependent mechanism.

3T3 Cells↗