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J A Gerlt

Publications and source records attributed to J A Gerlt.

70 records · Page 4Linked to original sources
PubMed1988

Identification of residues involved in a conformational change accompanying substitutions for glutamate-43 in staphylococcal nuclease.

A recent paper from our laboratories [Hibler, D. W., Stolowich, N. J., Reynolds, M. A., Gerlt, J. A. Wilde, J. A., & Bolton, P. H. (1987) Biochemistry 26, 6278] described the generation of site-directed substitutions for the putative general base Glu-43 in the active site of Staphylococcal nuclease (SNase) and the use of 1H NMR spectroscopy to characterize the effect of the substitutions on the conformations of the mutant proteins. The replacements for Glu-43 (Asp, Gln, Asn, Ser, and Ala) both decreased the catalytic efficiency and changed the one- and two-dimensional NMR spectral properties of the mutant enzymes. We have prepared and studied the NMR spectral properties of several samples of deuteriated wild-type SNase that allow sequence-specific resonance assignments for several aromatic and aliphatic amino acid side chains that experience changes both in normal one-dimensional spectra and in two-dimensional NOESY spectra. Due to severe spectral congestion of resonances in the one- and two-dimensional spectra of protiated SNase, the assignments would have been difficult, if not impossible, to obtain without deuteriation of selected amino acids. The spectra we have obtained demonstrate that changes in NOE intensities involve a valine residue that is spatially adjacent to two phenylalanine residues; given the X-ray structure for SNase [Cotton, F. A., Hazen, E. E., & Legg, M. J. (1979) Proc. Natl. Acad. Sci. U.S.A. 76, 2551], these residues must be Val-74, Phe-34, and Phe-76. In addition, a leucine residue experiencing changes in NOE intensities spatially adjacent to Val-74 and Phe-34 can be assigned to Leu-25.(ABSTRACT TRUNCATED AT 250 WORDS)

Binding Sites↗
PubMed1988

Cloning, DNA sequence analysis, and expression in Escherichia coli of the gene for mandelate racemase from Pseudomonas putida.

The gene for mandelate racemase (EC 5.1.2.2) from Pseudomonas putida (ATCC 12633) was cloned in Pseudomonas aeruginosa (ATCC 15692). The selection for the cloned gene was based upon the inability of P. aeruginosa to grow on (R)-mandelate as sole carbon source by virtue of the absence of mandelate racemase in its mandelate pathway. Fragments of P. putida DNA obtained by digestion of chromosomal DNA with Sau3A were ligated into the BamHI site of the Gram-negative vector pKT230 and transformed into the P. aeruginosa host. A transformant able to utilize (R)-mandelate as sole carbon source was characterized, and the plasmid was found to contain approximately five kilobase pairs of P. putida DNA. Subcloning of this DNA revealed the position of the gene for the racemase within the cloned DNA from P. putida. The dideoxy-DNA sequencing procedure was used to determine the sequence of the gene and its translated sequence. The amino acid sequence and molecular weight for mandelate racemase deduced from the gene sequence (38 570) are in excellent agreement with amino acid composition and molecular weight data for the polypeptide recently determined with enzyme isolated from P. putida; these recent determinations of the polypeptide molecular weight differ significantly from the originally reported value of 69,500 [Fee, Judith A., Hegeman, G.D., & Kenyon, G.L. (1974) Biochemistry 13,2528], which was used to demonstrate that alpha-phenylglycidate, an active site directed irreversible inhibitor, binds to the enzyme with a stoichiometry of 1:1.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1987

Site-directed mutants of staphylococcal nuclease. Detection and localization by 1H NMR spectroscopy of conformational changes accompanying substitutions for glutamic acid-43.

The high-resolution X-ray crystal structure of staphylococcal nuclease suggests that the gamma-carboxylate group of Glu-43 is directly involved in catalysis as a general base that facilitates the attack of water on the substrate phosphodiester. We have used primer-directed, site-specific mutagenesis to generate aspartate, glutamine, asparagine, alanine, and serine substitutions for this residue. The Vmax/Km for the aspartate mutant is reduced 1400-fold and the values for the charge-neutral mutations are reduced 5000-fold relative to the wild-type enzyme. Although these reductions in catalytic efficiency might appear useful in quantitatively estimating the importance of general basic catalysis in the reaction catalyzed by the wild-type enzyme, the thermal stabilities and 1H NMR spectral properties of the mutants suggest that such interpretations are ambiguous. All five mutants have higher melting temperatures for thermal denaturation than the wild-type enzyme, suggesting that the mutants have enhanced thermal stabilities relative to the wild-type enzyme. Chemical shift changes relative to the wild type are observed in both the aromatic and upfield-shifted methyl group regions of the 1H NMR spectra of the aspartate and serine mutants, suggesting the presence of conformational differences between the wild-type and mutant enzymes. That these conformational differences may be large enough to be mechanistically relevant is suggested by comparisons of the magnitudes of nuclear Overhauser effect (NOE) correlations between the aromatic and upfield-shifted methyl group regions observed via two-dimensional nuclear Overhauser effect correlation spectroscopy.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed1985

Thermal denaturation of staphylococcal nuclease.

The fully reversible thermal denaturation of staphylococcal nuclease in the absence and presence of Ca2+ and/or thymidine 3',5'-diphosphate (pdTp) from pH 4 to 8 has been studied by high-sensitivity differential scanning calorimetry. In the absence of ligands, the denaturation is accompanied by an enthalpy change of 4.25 cal g-1 and an increase in specific heat of 0.134 cal K-1 g-1, both of which are usual values for small globular proteins. The temperature (tm) of maximal excess specific heat is 53.4 degrees C. Each of the ligands, Ca2+ and pdTp, by itself has important effects on the unfolding of the protein which are enhanced when both ligands are present. Addition of saturating concentrations of these ligands raises the denaturational enthalpy to 5.74 cal g-1 in the case of Ca2+ and to 6.72 cal g-1 in the case of pdTp. The ligands raise the tm by as much as 11 degrees C depending on ligand concentration. From the variation of the denaturational enthalpies with ligand concentrations, binding constants at 53 degrees C equal to 950 M-1 and 1.4 X 10(4) M-1 are estimated for Ca2+ and pdTp, respectively, and from the enthalpies at ligand saturation, binding enthalpies at 53 degrees C of -15.0 and -19.3 kcal mol-1.

Calorimetry↗
PubMed1985

The ompA signal peptide directed secretion of Staphylococcal nuclease A by Escherichia coli.

The hybrid pre-enzyme formed by fusion of the signal peptide of the OmpA protein, a major outer membrane protein of Escherichia coli, to Staphylococcal nuclease A, a protein secreted by Staphylococcus aureus, is translocated across the cytoplasmic membrane of E. coli with concomitant cleavage of the signal peptide. A DNA fragment containing the coding sequence for the ompA signal peptide was initially ligated to a DNA fragment containing the coding sequence for nuclease A, with a linker sequence of 33 nucleotides separating the coding sequences. When this fused gene was induced, an enzymatically active nuclease was secreted into the periplasmic space; sequential Edman degradation of this protein revealed that the ompA signal peptide was removed at its normal cleavage site resulting in a modified version of the nuclease having 11 extra amino acid residues attached to the amino terminus of nuclease A. The 33 nucleotides between the coding sequences for the ompA signal peptide and the structural gene for nuclease A were subsequently deleted by synthetic oligonucleotide-directed site-specific mutagenesis. The nuclease produced by this hybrid gene was secreted into the periplasmic space and by sequential Edman degradation was identical to nuclease A. Thus, the ompA signal peptide is able to direct the secretion of fused staphylococcal nuclease A, and signal peptide processing occurs at the normal cleavage site. When the hybrid gene is expressed under the control of the lpp promoter, nuclease A is produced to the extent of 10% of the total cellular protein.

Amino Acid Sequence↗
PubMed1984

Syntheses and configurational analyses of thymidine 4-nitrophenyl [17O,18O]phosphates and the stereochemical course of a reaction catalyzed by bovine pancreatic deoxyribonuclease I.

The syntheses of both diastereomers of thymidine 3'-(4-nitrophenyl [17O,18O]phosphate) [( 17O,18O]TpNP) and of thymidine 5'-(4-nitrophenyl [17O,18O]phosphate) [( 17O,18O]NPpT) and the Rp diastereomer of thymidine 3'-(4-nitrophenyl [17O,18O]phosphate) 5'-(4-nitrophenyl phosphate) [( 17O,18O]NPpTpNP) are described. The absolute configurations of the chiral phosphorus atoms have been determined unambiguously by 31P and 17O NMR spectroscopy. The Rp diastereomer of [17O,18O]NPpTpNP was hydrolyzed in the presence of bovine pancreatic deoxyribonuclease I to yield the Rp diastereomer of thymidine 3'-[16O,17O,18O]-phosphate 5'-(4-nitrophenyl phosphate), demonstrating that the enzyme-catalyzed reaction occurs by a mechanism in which a single displacement reaction occurs at the chiral phosphorus atom.

Animals↗
PubMed1983

Evidence for a small catalytic domain in the adenylate cyclase from Salmonella typhimurium.

Deletions of large portions of the carboxyl-terminal end of the adenylate cyclase (ATP pyrophosphate lyase (cyclizing), EC 4.6.1.1) from Salmonella typhimurium do not significantly affect the enzymatic activity exhibited by the shortened polypeptide. The deletion mutations were generated by nuclease Bal31 digestion from the 3'-end of the cya gene fragment cloned by Wang et al. (Wang, J. Y.-J., Clegg, D. O., and Koshland, D.E. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 4684-4688); the shortened cya genes were inserted in pBR322 and used to transform a cya- strain of Escherichia coli. The original gene fragment encodes for an enzymatically active polypeptide having an apparent molecular weight of 77,000. Mutant polypeptides as small as 46,000 Da were found to retain significant enzymatic activity and to confer several cya+ phenotypes on the E. coli host. More extensive deletions resulting in polypeptides as small as 33,000 Da did not have assayable amounts of adenylate cyclase activity, but the biochemical properties of the transformed cya- host implicate the presence of low levels of enzymatic activity. These data suggest that the structure of the intact enzyme is composed of discrete functional domains. Such a structure for this adenylate cyclase should both facilitate investigations of the chemical mechanism of the reaction and allow structure-function relationships in this physiologically important enzyme to be investigated on a molecular level.

Adenylyl Cyclases↗
PubMed1983

Oxygen chiral phosphate esters.

During the past four years, methods have been reported for the syntheses and configurational analyses of virtually any phosphate mono- and diester chiral by virtue of oxygen isotope substitution, and these techniques have already been applied to an impressive number of enzymic and chemical reactions. At present, no experimental information is available that contradicts the simplest interpretations that have been applied to the results obtained for enzymic reactions: inversion of configuration indicating a direct displacement of the leaving group by the attacking group, and retention of configuration implying the formation of a phosphorylated or nucleotidylated enzyme intermediate. However, it does seem necessary to further investigate the mechanisms of at least some of the reactions discussed in this review to ensure that the simplest interpretation is correct. For example, the caveat we have raised about the interpretation of inversions of configurations in phosphohydrolase reactions is chemically reasonable, and these reactions should be reexamined to evaluate the importance of covalent catalysis by carboxylate groups. However, for the vast majority of the enzymic reactions that have been investigated, the stereochemical approach to ascertaining whether catalysis involves the formation of covalent intermediates remains the simplest and most direct method.

Binding Sites↗
PubMed1981

Stereochemical course of the hydrolysis of thymidine 5'-(4-nitrophenyl [17O,18O]phosphate) in H216O catalyzed by the phosphodiesterase from snake venom.

The phosphodiesterase from snake venom catalyzes the hydrolysis of the Rp diastereomer of thymidine 5'-(4-nitrophenyl [17O,18O]phosphate) in H216O with retention of configuration at phosphorus. This result is in agreement with those previously reported for the hydrolysis of chiral phosphorothioate substrates (Bryant, F. R., and Benkovic, S. J. (1979) Biochemistry 18, 2825-2828; Burgers, P. M. J., Eckstein, F., and Hunneman, D. H. (1979) J. Biol. Chem. 254, 7476-7478). The hydrolysis reaction catalyzed by this enzyme occurs via formation of a covalent nucleotidylated enzyme intermediate.

Animals↗
PubMed1980

Mechanism of the adenylate cyclase reaction. Stereochemistry of the reaction catalyzed by the enzyme from Brevibacterium liquefaciens.

Adenylate cyclase from Brevibacterium liquefaciens (ATCC 14929) catalyzes the formation of the RP-diastereomer of adenosine 3':5'-cyclic monophosphorothioate from the SP-diastereomer of adenosine-5'-(1-thiotriphosphate). The reaction catalyzed by this adenylate cyclase proceeds with inversion of configuration at phosphorus, indicating that the cyclization reaction is direct and does not involve formation of an adenylated enzyme intermediate.

Adenylyl Cyclases↗
PubMed1979

Stereochemistry of the hydrolysis of the endo isomer of uridine 2',3'-cyclic phosphorothioate catalyzed by the nonspecific phosphohydrolase from Enterobacter aerogenes.

The nonspecific phosphohydrolase from Enterobacter aerogenes (ATCC 13048) requires divalent metal ions for activity, since zinc present in the isolated enzyme can be removed by extensive dialysis against 8-hydroxyquinoline-5-sulfonate at pH 7.5 to yield an inactive enzyme which can be reactivated by addition of Zn2+, Cd2+, Co2+, Mn2+, or Ni2+; six ions of either zinc or cadmium can be incorporated into the inactive enzyme, and this incorporation of metal ion can be correlated with the regaining of activity (J. A. Gerlt, R. Dhesi, and H. C. Hemmings, unpublished experiments). The cadmium-reactivated phosphohydrolase catalyzes the hydrolysis of the endo isomer of uridine 2',3'-cyclic phosphorothioate (U greater than pS) to yield uridine 3'-monophosphorothioate as the major product. After enzymatic hydrolysis of the cyclic phosphorothioate in 19.8% H218O and chemical recyclization of the 18O-labeled acyclic phosphorothioates to yield a mixture of the endo and exo isomers of U greater than pS, 18O is found primarily in the exo isomer, as judged by examination of the 145.7-MHz phosphorus-31 nuclear magnetic resonance spectrum of the mixture. This observation indicates that the cadmium phosphosphohydrolase catalyzes hydrolysis of endo-U greater than pS with inversion of configuration, implying that the hydrolysis reaction proceeds by an in-line attack of water on the phosphorus.

Enterobacter↗
PubMed1975

Purification and properties of a phosphohydrolase from Enterobacter aerogenes.

A phosphohydrolase from Enterobacter aerogenes which hydrolyzes phosphate mono- and diesters has been purified approximately 50-fold to apparent homoeneity and crystallized. The enzyme is produced when the bacteria utilize phosphate diesters as sole phosphorus source. From sedimentation equilibrium experiments the molecular weight of the native enzyme is 173,000; from sodium dodecyl sulfate polyacrylamide gel electrophoresis the subunit molecular weight is 29,000, indicating that the enzyme is hexameric. The hydrolytic activity of the enzyme using both mono- and diesters is maximal at pH 5; THE Km of the enzyme for bis-p-nitrophenyl phosphate is constant from pH 5 to 8.5 whereas that for p-nitrophenyl phosphate increases about 40-fold as the pH increases over the same range. The phosphodiesterase activity is not inhibited by chelating agents but is inhibited by several divalent metal ions. 31-P NMR spectroscopy was used to identify the hydrolysis products of glycoside cyclic phosphates. The enzyme-catalyzed hydrolysis of methyl beta-D-ribofuranoside cyclic 3:5-phosphate yields exclusively the 5-phosphate whereas that of adenosine 3:5-monophosphate yields a 4:1 mixture of 3- and 5- AMP.

4-Nitrophenylphosphatase↗
PubMed1975

The enthalpies of hydrolysis of acyclic, monocyclic, and glycoside cyclic phosphate diesters.

The enthalpies of hydrolysis of acyclic, monocyclic, and glycoside cyclic phosphate diesters have been measured by flow microcalorimetry using a phosphohydrolase isolated from Enterobacter aerogenes as catalyst. The values so obtained (kilocalories per mol) (at 25 degrees) for sodium salts are: diethyl phosphate, minus 1.8 plus or minus 0.5; ethylene phosphate, minus 6.4 plus or minus 0.2; trimethylene phosphate, minus 3.0 plus or minus 0.2; tetramethylene phosphate, minus 2.2 plus or minus 0.1; methyl beta-D-ribofuranoside cyclic 3:5-phosphate, minus 11.1 plus or minus 0.2; methyl alpha-D-glucopyranoside cyclic 4:6-phosphate, minus 6.3 plus or minus 0.1; and cyclic adenosine 3:5-monophosphate (5-ester bond), minus 11.1 plus or minus 0.4 (10-minus 3 M Mg-2+). The enthalpy of hydrolysis of the 3-ester bond of cyclic adenosine 3:5-monophosphate (10-minus 3 M Mg-2+) has been revised to minus 11.1 plus or minus 0.2 kcal/mol from the value of minus 13.2 plus or minus 0.4 kcal/mol reported previously (greengard, p., rudolph, s.a., and sturtevant, j. m. (1969) j. biol. Chem. 244, 4798). All these values pertain to the hydrolysis of singly charged diesters to form singly charged monoesters. The data for the acyclic and monocyclic phosphodiesters are in qualitative agreement with their hydrolytic reactivities. The enthalpies measured for the hydrolysis of the glycoside cyclic phosphates cannot now be explained on the basis of their structures or reactivities; perhaps a contribution to the enthalpies by solvation or a previously unrecognized geometric strain effect may be responsible for the large exothermic enthalpies of these cyclic phosphate diesters. Changes in the heat capacity, increment Cp, for some of the hydrolytic reactions were also measured.

Cyclic AMP↗