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Full-Text Articles in Physical Sciences and Mathematics
The Aminopeptidase From Aeromonas Proteolytica Can Function As An Esterase, David Bienvenue, Rebecca Matthew, Dagmar Ringe, Richard Holz
The Aminopeptidase From Aeromonas Proteolytica Can Function As An Esterase, David Bienvenue, Rebecca Matthew, Dagmar Ringe, Richard Holz
Richard C. Holz
The aminopeptidase from Aeromonas proteolytica (AAP) can catalyze the hydrolysis of L-leucine ethyl ester (L-Leu-OEt) with a rate of 96±5 s–1 and a K m of 700 µM. The observed turnover number for L-Leu-OEt hydrolysis by AAP is similar to that observed for peptide hydrolysis, which is 67±5 s–1. The k cat values for the hydrolysis of L-Leu-OEt and L-leucine-p-nitroanilide (L-pNA) catalyzed by AAP were determined at different pH values under saturating substrate concentrations. Construction of an Arrhenius plot from the temperature dependence of AAP-catalyzed ester hydrolysis indicates that the rate-limiting step does not change as a function of temperature …
Kinetic And Spectroscopic Characterization Of The E134a- And E134d-Altered Dape-Encoded N-Succinyl-L,L-Diaminopimelic Acid Desuccinylase From Haemophilus Influenzae, Ryan Davis, David Bienvenue, Sabina Swierczek, Danuta Gilner, Lakshman Rajagopal, Brian Bennett, Richard Holz
Kinetic And Spectroscopic Characterization Of The E134a- And E134d-Altered Dape-Encoded N-Succinyl-L,L-Diaminopimelic Acid Desuccinylase From Haemophilus Influenzae, Ryan Davis, David Bienvenue, Sabina Swierczek, Danuta Gilner, Lakshman Rajagopal, Brian Bennett, Richard Holz
Richard C. Holz
Glutamate-134 (E134) is proposed to act as the general acid/base during the hydrolysis reaction catalyzed by the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) from Haemophilus influenzae. To date, no direct evidence has been reported for the role of E134 during catalytic turnover by DapE. In order to elucidate the catalytic role of E134, altered DapE enzymes were prepared in which E134 was substituted with an alanine and an aspartate residue. The Michaelis constant (K m) does not change upon substitution with aspartate but the rate of the reaction changes drastically in the following order: glutamate (100% activity), aspartate (0.09%), and alanine …
The 1.20 Å Resolution Crystal Structure Of The Aminopeptidase From Aeromonas Proteolytica Complexed With Tris: A Tale Of Buffer Inhibition, William Desmarais, David Bienvenue, Krzysztof Bzymek, Richard Holz, Gregory Petsko, Dagmar Ringe
The 1.20 Å Resolution Crystal Structure Of The Aminopeptidase From Aeromonas Proteolytica Complexed With Tris: A Tale Of Buffer Inhibition, William Desmarais, David Bienvenue, Krzysztof Bzymek, Richard Holz, Gregory Petsko, Dagmar Ringe
Richard C. Holz
The aminopeptidase from Aeromonas proteolytica (AAP) is a bridged bimetallic enzyme that removes the N-terminal amino acid from a peptide chain. To fully understand the metal roles in the reaction pathway of AAP we have solved the 1.20 Å resolution crystal structure of native AAP (PDB ID = 1LOK). The high-quality electron density maps showed a single Tris molecule chelated to the active site Zn2+, alternate side chain conformations for some side chains, a sodium ion that mediates a crystal contact, a surface thiocyanate ion, and several potential hydrogen atoms. In addition, the high precision of the atomic …
Structural Basis For Catalysis By The Mono- And Dimetalated Forms Of The Dape-Encoded N-Succinyl-L,L-Diaminopimelic Acid Desuccinylase, Boguslaw Nocek, Danuta Gillner, Yao Fan, Richard Holz, Andzrej Joachimiak
Structural Basis For Catalysis By The Mono- And Dimetalated Forms Of The Dape-Encoded N-Succinyl-L,L-Diaminopimelic Acid Desuccinylase, Boguslaw Nocek, Danuta Gillner, Yao Fan, Richard Holz, Andzrej Joachimiak
Richard C. Holz
Biosynthesis of lysine and meso-diaminopimelic acid in bacteria provides essential components for protein synthesis and construction of the bacterial peptidoglycan cell wall. The dapE operon enzymes synthesize both meso-diaminopimelic acid and lysine and, therefore, represent potential targets for novel antibacterials. The dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase functions in a late step of the pathway and converts N-succinyl-l,l-diaminopimelic acid to l,l-diaminopimelic acid and succinate. Deletion of the dapE gene is lethal to Helicobacter pylori and Mycobacterium smegmatis, indicating that DapE's are essential for cell growth and proliferation. Since there are no similar pathways in humans, inhibitors …
Structural Characterization Of Zn(Ii)-, Co(Ii)-, And Mn(Ii)-Loaded Forms Of The Arge-Encoded N-Acetyl-L-Ornithine Deacetylase From Escherichia Coli, Ye Tao, Jacob Shokes, Wade Mcgregor, Robert Scott, Richard Holz
Structural Characterization Of Zn(Ii)-, Co(Ii)-, And Mn(Ii)-Loaded Forms Of The Arge-Encoded N-Acetyl-L-Ornithine Deacetylase From Escherichia Coli, Ye Tao, Jacob Shokes, Wade Mcgregor, Robert Scott, Richard Holz
Richard C. Holz
The Zn, Co, and Mn K-edge extended X-ray absorption fine structure (EXAFS) spectra of the N-acetyl-l-ornithine deacetylase (ArgE) from Escherichia coli, loaded with one or two equivalents of divalent metal ions (i.e., [Zn(II)_(ArgE)], [Zn(II)Zn(II)(ArgE)], [Co(II)_(ArgE)], [Co(II)Co(II)(ArgE)], [Mn(II)_(ArgE)], and [Mn(II)Mn(II)(ArgE)]), were recorded. The Fourier transformed data (FT) for [Zn(II)_(ArgE)], [Zn(II)Zn(II)(ArgE)], [Co(II)_(ArgE)] and [Co(II)Co(II)(ArgE)] are dominated by a peak at 2.05 Å, that can be fit assuming five or six light atom (N,O) scatterers. Inclusion of multiple-scattering contributions from the outer-shell atoms of a histidine-imidazole ring resulted in reasonable Debye–Waller factors for these contributions and a slight reduction in the goodness-of-fit value …