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D B McKay

Publications and source records attributed to D B McKay.

At least 19 recordsLinked to original sources
PubMed2001

A gene, cobA + hemD, from Selenomonas ruminantium encodes a bifunctional enzyme involved in the synthesis of vitamin B12.

Coenzymes derived from vitamin B12 (cyanocobalamin) are particularly important for core metabolism in ruminant animals. Selenomonas ruminantium, a Gram-positive obligate anaerobe isolated from cattle, is the main contributor of vitamin B12 to such ruminant animals. In nature, there are both aerobic and anaerobic pathways for B12 synthesis - the latter is only partly elucidated. Until now, there has been no investigation of B12 synthesis in S. ruminantium, which must use an anaerobic pathway. This paper reports the cloning of the chromosomal operon from S. ruminantium which is responsible for the first committed steps in corrinoid synthesis. Five open reading frames were found in the cloned fragment. All deduced amino acid sequences had similarity to defined proteins in the databases that are involved in porphyrin and corrin synthesis. Of particular interest is the gene designated cobA + hemD, which encodes a single polypeptide possessing two catalytic functions - uroporphyrinogen III synthase and uroporphyrinogen III 2,7-methyltransferase. This enzyme converts hydroxymethylbilane to precorrin-2. The functions of the protein coded by cobA + hemD were established by heterologous expression in Escherichia coli. The CobA activity has been demonstrated for three distinct types of proteins - monofunctional, bifunctional with siroheme formation and, this report, bifunctional with uroporphyrinogen III synthesis. The type found in S. ruminantium (cobA + hemD) is probably restricted to obligately anaerobic fermentative bacteria.

Alkyl and Aryl Transferases↗
PubMed2001

Refined crystallographic structure of Pseudomonas aeruginosa exotoxin A and its implications for the molecular mechanism of toxicity.

Exotoxin A of Pseudomonas aeruginosa asserts its cellular toxicity through ADP-ribosylation of translation elongation factor 2, predicated on binding to specific cell surface receptors and intracellular trafficking via a complex pathway that ultimately results in translocation of an enzymatic activity into the cytoplasm. In early work, the crystallographic structure of exotoxin A was determined to 3.0 A resolution, revealing a tertiary fold having three distinct structural domains; subsequent work has shown that the domains are individually responsible for the receptor binding (domain I), transmembrane targeting (domain II), and ADP-ribosyl transferase (domain III) activities, respectively. Here, we report the structures of wild-type and W281A mutant toxin proteins at pH 8.0, refined with data to 1.62 A and 1.45 A resolution, respectively. The refined models clarify several ionic interactions within structural domains I and II that may modulate an obligatory conformational change that is induced by low pH. Proteolytic cleavage by furin is also obligatory for toxicity; the W281A mutant protein is substantially more susceptible to cleavage than the wild-type toxin. The tertiary structures of the furin cleavage sites of the wild-type and W281 mutant toxins are similar; however, the mutant toxin has significantly higher B-factors around the cleavage site, suggesting that the greater susceptibility to furin cleavage is due to increased local disorder/flexibility at the site, rather than to differences in static tertiary structure. Comparison of the refined structures of full-length toxin, which lacks ADP-ribosyl transferase activity, to that of the enzymatic domain alone reveals a salt bridge between Arg467 of the catalytic domain and Glu348 of domain II that restrains the substrate binding cleft in a conformation that precludes NAD+ binding. The refined structures of exotoxin A provide precise models for the design and interpretation of further studies of the mechanism of intoxication.

ADP Ribose Transferases↗
PubMed2001

Structure of Haemophilus influenzae HslV protein at 1.9 A resolution, revealing a cation-binding site near the catalytic site.

The structure of the Haemophilus influenzae HslV protease of the HslUV 'prokaryotic proteasome' has been solved by molecular replacement and refined with data to 1.9 A resolution. The protease is a 'double donut' of hexameric rings; two alternative sets of intermolecular interactions between protomers in the rings result in 'quasi-equivalent' packing within the assembly. Anomalous scattering data from crystals with potassium present in the mother liquor reveal a K(+) ion bound with octahedral coordination near the active-site Thr1 residue. The site also binds Na(+) ions and is likely to bind Mg(2+), suggesting that monovalent and divalent metal ions may influence the catalytic activity of the protease.

ATP-Dependent Proteases↗
PubMed2001

Structure of Haemophilus influenzae HslU protein in crystals with one-dimensional disorder twinning.

The structure of the Haemophilus influenzae HslU protein, a molecular chaperone of the Clp/Hsp100 family, has been solved to 2.3 A by molecular replacement using a model of the homologous Escherichia coli protein. The crystals in which the structure was solved have an unusual twinning, or one-dimensional disorder, in which each successive crystal-packing layer is displaced laterally relative to the one below it. A model for the twinning and an algorithm for detwinning the data are described. It is known from other work that when the HslU hexamer binds its cognate protease HslV, the carboxy-terminal helices of HslU protomers distend and bind between HslV subunits. Comparison of HslU alone with its structure in the HslUV complex reveals several conserved amino-acid residues whose side-chain interactions differ between the two structures, suggesting that they may be part of a conformational switch that facilitates the release of the HslU carboxy-terminal helices when HslV binds.

ATP-Dependent Proteases↗
PubMed2001

Receptor protection studies to characterize neuronal nicotinic receptors: tubocurarine prevents alkylation of adrenal nicotinic receptors.

Our laboratory has evidence that multiple nicotinic acetylcholine receptor subtypes regulate bovine adrenal catecholamine release. In the following studies, receptor protection assays were used to differentiate adrenal nicotinic receptor subpopulations. Under alkylating conditions, bromoacetylcholine (30 microM) reduced nicotinic receptor-stimulated adrenal catecholamine secretion by approximately 80%. When 100 microM tubocurarine was present during alkylation, nicotine-stimulated secretion was reduced by less than 30%. Hexamethonium (500 microM), decamethonium (500 microM), mecamylamine (50 microM), pentolinium (50 microM), adiphenine (50 microM), methyllycaconitine (1 microM) and alpha-bungarotoxin (1 microM) afforded no protection when present during alkylation. When the pharmacology of residual, tubocurarine-protected receptors was investigated, the EC50 value for nicotine's stimulatory effects on secretion significantly increased from 4.0 (2.5-6.5) microM in control cells to 9.1 (7.2-11.4) microM in tubocurarine-protected cells. In addition, the IC50 value for tubocurarine's inhibitory effects on release significantly decreased from 0.7 (0.5-0.9) microM in control cells to 0.3 (0.2-0.4) microM in tubocurarine-protected cells. These studies support the use of protection assays to characterize nicotinic receptor subpopulations.

Acetylcholine↗
PubMed2001

Analysis of the pobA and pobR genes controlling expression of p-hydroxybenzoate hydroxylase in Azotobacter chroococcum.

We report the cloning and analysis of a gene and its cognate regulatory element from a member of the Azotobacteriaceae which are involved in the breakdown of an aromatic compound. The genes from Azotobacter chroococcum encoding p-hydroxybenzoate hydroxylase (pobA) and its regulatory protein (pobR) were cloned from a genomic library and sequenced. Sequence analysis of pobA revealed homology with other bacterial p-hydroxybenzoate hydroxylase enzymes. Residues essential to the structure and function of the enzyme have been conserved. The pobR gene encodes a DNA binding regulatory protein with similarity to proteins from the AraC/XylS family of transcriptional activators. A fragment containing both pobA and pobR was cloned into pUC19 and p-hydroxybenzoate hydroxylase activity was induced in Escherichia coli by the addition of p-hydroxybenzoate. A frame-shift mutation introduced into the pobR gene prevented expression of p-hydroxybenzoate hydroxylase, indicating that PobR is the protein required for transcription of pobA. Interestingly, A. chroococcum PobR has no homology to the PobR protein that is the transcriptional activator of pobA in Acinetobacter strain ADP1, a protein that is homologous to the IclR family of transcriptional regulators. However, PobR from A. chroococcum is homologous to several other proteins, suggesting that these proteins will also function as transcriptional activators of pobA.

4-Hydroxybenzoate-3-Monooxygenase↗
PubMed2001

Structure of the universal stress protein of Haemophilus influenzae.

BACKGROUND: The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced several-fold when cellular viability is challenged with heat shock, nutrient starvation, stress agents which arrest cell growth, or DNA-damaging agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, suggesting that it asserts a general "stress endurance" activity. However, neither the structure of UspA nor the biochemical mechanism by which it protects cells from the broad spectrum of stress agents is known. RESULTS: The crystal structure of Haemophilus influenzae UspA reveals an asymmetric dimer with a tertiary alpha/beta fold similar to that of the Methanococcus jannaschi MJ0577 protein, a protein whose crystal structure revealed a novel ATP binding motif. UspA differs significantly from the MJ0577 structure in several details, including the triphosphate binding loop of the ATP binding motif; UspA shows no ATP binding activity. CONCLUSIONS: Within the universal stress protein family that is delineated by sequence similarity, UspA is the only member which has been correlated with a cellular activity, and MJ0577 is the only member which has been assigned a biochemical activity, i.e., ATP binding. UspA has a similar fold to the MJ0577 protein but does not bind ATP. This suggests that members of this protein family will segregate into two groups, based on whether or not they bind ATP. By implication, one subset of the universal stress proteins presumably has an ATP-dependent function, while another subset functions in ATP-independent activities.

Adenosine Triphosphate↗
PubMed2001

Identification of cyanobacteria and their toxigenicity in environmental samples by rapid molecular analysis.

We report molecular analyses which identify cyanobacterial strains present in environmental samples. These analyses do not require the isolation and culture of strains. Identification of cyanobacteria used the polymerase chain reaction (PCR), based on the phycocyanin operon. Differentiation was either by restriction endonuclease digestion (restriction fragment length polymorphisms) or sequencing of the PCR products. Identification was based on sequence homology of the intergenic spacer region (IGS) between the beta- and alpha-phycocyanin subunits (PC-IGS) with database records. We have found that the length and sequence of the PC-IGS is capable of predicting the genus accurately, but not the species. Toxigenicity was determined with oligonucleotide probes for key steps in the microcystin toxin synthesis pathway. We have shown that it is possible to easily and routinely obtain PCR amplification products and differentiate the strains in bloom samples. The methods can detect even minor components in bloom samples, which may not be apparent on microscopic examination. Genetic probes for microcystin toxigenicity are effective on environmental samples, eliminating the need for isolation and culture of the organisms. The use of a suite of tests described here will allow water managers to determine the presence and the type of cyanobacteria and their microcystin toxigenicity.

Animals↗
PubMed2000

Effects of sulfhydryl modification on adrenal nicotinic acetylcholine receptors: disulfide integrity is not essential for activation.

The importance of disulfide bridges in muscle nicotinic receptors is well established; however, for neuronal nicotinic receptors, the effects of sulfhydryl modification are less definitive. In these studies the effects of treatment with the mild reducing agent, dithiothreitol, on adrenal nicotinic receptors are described. We have found that following dithiothreitol treatment, adrenal chromaffin cells retained the ability to be stimulated by a variety of nicotinic receptor agonists including nicotine, acetylcholine, cytisine, epibatidine, and bromoacetylcholine. However, with dithiothreitol treatment, changes in apparent affinities were seen with two agonists, epibatidine and bromoacetylcholine. These effects of dithiothreitol on apparent affinities were concentration-dependent and reversible upon treatment with an oxidizing agent. Dithiothreitol treatment also produced effects on secretion that were independent of nicotinic receptor activation. Our results are unlike those in other tissues containing nicotinic receptors and suggest that subunit composition of nicotinic receptors influences the functional outcome of sulfhydryl modification.

Adrenal Glands↗
PubMed2000

Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase.

The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family, a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. Previous work has provided the structure of the amino-terminal, ATP-binding domain of eIF4A. Extending those results, we have solved the structure of the carboxyl-terminal domain of eIF4A with data to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases. Using data to 2.8 A resolution and molecular replacement with the refined model of the carboxyl-terminal domain, we have completed the structure of full-length eIF4A; it is a "dumbbell" structure consisting of two compact domains connected by an extended linker. By using the structures of other helicases as a template, compact structures can be modeled for eIF4A that suggest (i) helicase motif IV binds RNA; (ii) Arg-298, which is conserved in the DEA(D/H)-box RNA helicase family but is absent from many other helicases, also binds RNA; and (iii) motifs V and VI "link" the carboxyl-terminal domain to the amino-terminal domain through interactions with ATP and the DEA(D/H) motif, providing a mechanism for coupling ATP binding and hydrolysis with conformational changes that modulate RNA binding.

Amino Acid Sequence↗
PubMed2000

Crystal and solution structures of an HslUV protease-chaperone complex.

HslUV is a "prokaryotic proteasome" composed of the HslV protease and the HslU ATPase, a chaperone of the Clp/Hsp100 family. The 3.4 A crystal structure of an HslUV complex is presented here. Two hexameric ATP binding rings of HslU bind intimately to opposite sides of the HslV protease; the HslU "intermediate domains" extend outward from the complex. The solution structure of HslUV, derived from small angle X-ray scattering data under conditions where the complex is assembled and active, agrees with this crystallographic structure. When the complex forms, the carboxy-terminal helices of HslU distend and bind between subunits of HslV, and the apical helices of HslV shift substantially, transmitting a conformational change to the active site region of the protease.

ATP-Dependent Proteases↗
PubMed1999

Antigen-induced unresponsiveness results in altered T cell signaling.

Pretransplant exposure to allogeneic lymphocytes can result in donor-specific unresponsiveness and prolonged allograft survival. Intracellular signaling events have been described in anergic T cell clones, but the biochemical events underlying in vivo induced unresponsiveness have not been studied in detail. We employed a TCR transgenic mouse, bearing the 2C TCR, providing adequate numbers of homogenous peripheral T cells to study biochemical aspects of T cell unresponsiveness in vivo. 2C mice exposed to semiallogeneic lymphocytes (H-2b x H-2d) experienced prolonged H-2d cardiac allograft survival, and cells from these mice did not proliferate or make IL-2 in response to alloantigen (H-2d). Importantly, there were marked differences in TCR-associated tyrosine phosphorylation activation patterns. The targets for the unresponsive state appear to be diminished Lck activation and absent ZAP-70 and LAT (linker for activation of T cells) phosphorylation. Our study demonstrates that Ag-induced tolerance in vivo is accompanied by altered early TCR-mediated signaling events.

Animals↗
PubMed1999

Mapping the role of active site residues for transducing an ATP-induced conformational change in the bovine 70-kDa heat shock cognate protein.

ATP binding induces a conformational change in 70-kDa heat shock proteins (Hsp70s) that facilitates release of bound polypeptides. Using the bovine heat shock cognate protein (Hsc70) as a representative of the Hsp70 family, we have characterized the effect of mutations on the coupling between ATP binding and the nucleotide-induced conformational change. Steady-state solution small-angle X-ray scattering and kinetic fluorescence measurements on a 60-kDa fragment of Hsc70 show that point mutations K71M, E175S, D199S, and D206S in the nucleotide binding cleft impair the ability of ATP to induce a conformational change. A secondary mutation in the peptide binding domain, E543K, "rescues" the ATP-induced transition for three of these mutations (E175S/E543K, D199S/E543K, and D206S/E543K) but not for K71M/E543K. Analysis of kinetics of the ATPase cycle confirm that these effects do not result from unexpectedly rapid ATP hydrolysis or slow ATP binding. Crystallographic structures of E175S, D199S, and D206S mutant ATPase fragment proteins show that the mutations do not perturb the tertiary structure of the protein but do significantly alter the protein-ligand interactions, due in part to an apparent charge compensation effect whereby mutating a (probably) negatively charged carboxyl group to a neutral serine displaces a K+ ion from the nucleotide binding cleft in two out of three cases (E175S and D199S but not D206S).

Adenosine Triphosphatases↗
PubMed1999

Crystallographic structure of the amino terminal domain of yeast initiation factor 4A, a representative DEAD-box RNA helicase.

The eukaryotic translation initiation factor 4A (elF4A) is a representative of the DEAD-box RNA helicase protein family. We have solved the crystallographic structure of the amino-terminal domain (residues 1-223) of yeast elF4A. The domain is built around a core scaffold, a parallel alpha-beta motif with five beta strands, that is found in other RNA and DNA helicases, as well as in the RecA protein. The amino acid sequence motifs that are conserved within the helicase family are localized to the beta strand-->alpha helix junctions within the core. The core of the amino terminal domain of elF4A is amplified with additional structural elements that differ from those of other helicases. The phosphate binding loop (the Walker A motif) is in an unusual closed conformation. The crystallographic structure reveals specific interactions between amino acid residues of the phosphate binding loop, the DEAD motif, and the SAT motif, whose alteration is known to impair coupling between the ATPase cycle and the RNA unwinding activity of elF4A.

Amino Acid Sequence↗
PubMed1999

Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis.

The leadzyme is a small RNA motif that catalyzes a site-specific, Pb2+-dependent cleavage reaction. As such, it is an example of a metal-dependent RNA enzyme. Here we describe the X-ray crystallographic structure of the leadzyme, which reveals two independent molecules per asymmetric unit. Both molecules feature an internal loop in which a bulged purine base stack twists away from the helical stem. This kinks the backbone, rendering the phosphodiester bond susceptible to cleavage. The independent molecules have different conformations: one leadzyme copy coordinates Mg2+, whereas the other binds only Ba2+ or Pb2+. In the active site of the latter molecule, a single Ba2+ ion coordinates the 2'-OH nucleophile, and appears to mimic the binding of catalytic lead. These observations allow a bond cleavage reaction to be modeled, which reveals the minimal structural features necessary for catalysis by this small ribozyme.

Base Sequence↗
PubMed1998

The hydroxyl of threonine 13 of the bovine 70-kDa heat shock cognate protein is essential for transducing the ATP-induced conformational change.

The mechanism by which ATP binding transduces a conformational change in 70-kDa heat shock proteins that results in release of bound peptides remains obscure. Wei and Hendershot demonstrated that mutating Thr37 of hamster BiP to glycine impeded the ATP-induced conformational change, as monitored by proteolysis [(1995) J. Biol. Chem. 270, 26670-26676]. We have mutated the equivalent resitude of the bovine heat shock cognate protein (Hsc70), Thr13, to serine, valine, and glycine. Solution small-angle X-ray scattering experiments on a 60-kDa fragment of Hsc70 show that ATP binding induces a conformational change in the T13S mutant but not the T13V or T13G mutants. The kinetics of ATP-induced tryptophan fluorescence intensity changes in the 60-kDa proteins is biphasic for the T13S mutant but monophasic for T13V or T13G, consistent with a conformational change following initial ATP binding in the T13S mutant but not the other two. Crystallographic structures of the ATPase fragments of the T13S and T13G mutants at 1.7 A resolution show that the mutations do not disrupt the ATP binding site and that the serine hydroxyl mimics the threonine hydroxyl in the wild-type structure. We conclude that the hydroxyl of Thr13 is essential for coupling ATP binding to a conformational change in Hsc70. Molecular modeling suggests this may result from the threonine hydroxyl hydrogen-bonding to a gamma-phosphate oxygen of ATP, thereby inducing a structural shift within the ATPase domain that couples to its interactions with the peptide binding domain.

Adenosine Triphosphatases↗