Crystallographic and Enzymic Investigations on the Role of Ser558, His610, and Asn614 in the Catalytic Mechanism of Azotobacter vinelandii Dihydrolipoamide Acetyltransferase (E2p)

Biochemistry ◽  
1995 ◽  
Vol 34 (13) ◽  
pp. 4287-4298 ◽  
Author(s):  
Joerg Hendle ◽  
Andrea Mattevi ◽  
Adrie H. Westphal ◽  
Johan Spee ◽  
Arie de Kok ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Azotobacter Vinelandii

Role of Lys-226 in the Catalytic Mechanism ofBacillus StearothermophilusSerine HydroxymethyltransferaseCrystal Structure and Kinetic Studies†,‡

Biochemistry ◽  
2005 ◽  
Vol 44 (18) ◽  
pp. 6929-6937 ◽  
Author(s):  
Siddegowda Bhavani ◽  
V. Trivedi ◽  
V. R. Jala ◽  
H. S. Subramanya ◽  
Purnima Kaul ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Kinetic Studies

Study of the catalytic mechanism of a non-heme Fe catalyst: The role of the spin state of the iron

2021 ◽  
Vol 764 ◽  
pp. 138282
Author(s):  
Aikaterini Gemenetzi ◽  
Panagiota Stathi ◽  
Yiannis Deligiannakis ◽  
Maria Louloudi
Keyword(s):  
Spin State ◽  
Catalytic Mechanism ◽  
Fe Catalyst

Crystal structure of the wild-type and D30A mutant thioredoxin h of Chlamydomonas reinhardtii and implications for the catalytic mechanism

2001 ◽  
Vol 359 (1) ◽  
pp. 65-75 ◽  
Author(s):  
Valeria MENCHISE ◽  
Catherine CORBIER ◽  
Claude DIDIERJEAN ◽  
Michele SAVIANO ◽  
Ettore BENEDETTI ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Proton Transfer ◽  
Chlamydomonas Reinhardtii ◽  
Catalytic Mechanism ◽  
Structural Data ◽  
Careful Analysis ◽  
Wild Type ◽  
Thioredoxin H ◽  
Dynamics Simulations

Thioredoxins are ubiquitous proteins which catalyse the reduction of disulphide bridges on target proteins. The catalytic mechanism proceeds via a mixed disulphide intermediate whose breakdown should be enhanced by the involvement of a conserved buried residue, Asp-30, as a base catalyst towards residue Cys-39. We report here the crystal structure of wild-type and D30A mutant thioredoxin h from Chlamydomonas reinhardtii, which constitutes the first crystal structure of a cytosolic thioredoxin isolated from a eukaryotic plant organism. The role of residue Asp-30 in catalysis has been revisited since the distance between the carboxylate OD1 of Asp-30 and the sulphur SG of Cys-39 is too great to support the hypothesis of direct proton transfer. A careful analysis of all available crystal structures reveals that the relative positioning of residues Asp-30 and Cys-39 as well as hydrophobic contacts in the vicinity of residue Asp-30 do not allow a conformational change sufficient to bring the two residues close enough for a direct proton transfer. This suggests that protonation/deprotonation of Cys-39 should be mediated by a water molecule. Molecular-dynamics simulations, carried out either in vacuo or in water, as well as proton-inventory experiments, support this hypothesis. The results are discussed with respect to biochemical and structural data.

Structure−Function Relationships in Human Glutathione-Dependent Formaldehyde Dehydrogenase. Role of Glu-67 and Arg-368 in the Catalytic Mechanism†,‡

Biochemistry ◽  
2006 ◽  
Vol 45 (15) ◽  
pp. 4819-4830 ◽  
Author(s):  
Paresh C. Sanghani ◽  
Wilhelmina I. Davis ◽  
LanMin Zhai ◽  
Howard Robinson
Keyword(s):  
Structure Function ◽  
Catalytic Mechanism ◽  
Formaldehyde Dehydrogenase

scholarly journals A QM/MM Study of Acylphosphatase Reveals the Nucleophilic-Attack and Ensuing Carbonyl-Assisted Catalytic Mechanisms

2020 ◽  
Author(s):  
zheng zhao ◽  
Phil bourne ◽  
Hao Hu ◽  
Huanyu Chu
Keyword(s):  
Energy Barrier ◽  
Potential Energy Surfaces ◽  
Catalytic Mechanism ◽  
Interaction Networks ◽  
Nucleophilic Attack ◽  
Reaction Coordinates ◽  
Transition State Stabilization ◽  
Catalytic Mechanisms ◽  
Energy Surfaces

Acylphosphatase is one of the vital enzymes in many organs/tissues to catalyze an acylphosphate molecule into carboxylate and phosphate. Here we use a combined <i>ab initio</i> QM/MM approach to reveal the catalytic mechanism of the benzoylphosphate-bound acylphosphatase system. Using a multi-dimensional reaction-coordinates-driving scheme, we obtained a detailed catalytic process including one nucleophilic-attack and then an ensuing carbonyl-shuttle catalytic mechanism by calculating two-dimensional potential energy surfaces. We also obtained an experiment-agreeable energy barrier and validated the role of the key amino acid Asn38. Additionally, we qualified the transition state stabilization strategy based on the amino acids-contributed interaction networks revealed in the enzymatic environment. This study provided usefule insights into the underlying catalytic mechanism to contribute to disease-involved research.

Structural investigation of inhibitor designs targeting 3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis

2011 ◽  
Vol 436 (3) ◽  
pp. 729-739 ◽  
Author(s):  
Marcio V. B. Dias ◽  
William C. Snee ◽  
Karen M. Bromfield ◽  
Richard J. Payne ◽  
Satheesh K. Palaninathan ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Drug Targets ◽  
Structural Investigation ◽  
Catalytic Mechanism ◽  
Shikimate Pathway ◽  
Structural Rearrangement ◽  
Competitive Inhibitors ◽  
Structural Insights ◽  
Potential Drug Targets

The shikimate pathway is essential in Mycobacterium tuberculosis and its absence from humans makes the enzymes of this pathway potential drug targets. In the present paper, we provide structural insights into ligand and inhibitor binding to 3-dehydroquinate dehydratase (dehydroquinase) from M. tuberculosis (MtDHQase), the third enzyme of the shikimate pathway. The enzyme has been crystallized in complex with its reaction product, 3-dehydroshikimate, and with six different competitive inhibitors. The inhibitor 2,3-anhydroquinate mimics the flattened enol/enolate reaction intermediate and serves as an anchor molecule for four of the inhibitors investigated. MtDHQase also forms a complex with citrazinic acid, a planar analogue of the reaction product. The structure of MtDHQase in complex with a 2,3-anhydroquinate moiety attached to a biaryl group shows that this group extends to an active-site subpocket inducing significant structural rearrangement. The flexible extensions of inhibitors designed to form π-stacking interactions with the catalytic Tyr24 have been investigated. The high-resolution crystal structures of the MtDHQase complexes provide structural evidence for the role of the loop residues 19–24 in MtDHQase ligand binding and catalytic mechanism and provide a rationale for the design and efficacy of inhibitors.

scholarly journals Elucidating the role of metal ions in carbonic anhydrase catalysis

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jin Kyun Kim ◽  
Cheol Lee ◽  
Seon Woo Lim ◽  
Aniruddha Adhikari ◽  
Jacob T. Andring ◽  
...  
Keyword(s):  
Carbonic Anhydrase ◽  
Metal Ions ◽  
Metal Ion ◽  
Catalytic Mechanism ◽  
Chemical Properties ◽  
Water Network ◽  
Native Metal ◽  
Trigonal Bipyramidal ◽  
Electrostatic Effect

Abstract Why metalloenzymes often show dramatic changes in their catalytic activity when subjected to chemically similar but non-native metal substitutions is a long-standing puzzle. Here, we report on the catalytic roles of metal ions in a model metalloenzyme system, human carbonic anhydrase II (CA II). Through a comparative study on the intermediate states of the zinc-bound native CA II and non-native metal-substituted CA IIs, we demonstrate that the characteristic metal ion coordination geometries (tetrahedral for Zn2+, tetrahedral to octahedral conversion for Co2+, octahedral for Ni2+, and trigonal bipyramidal for Cu2+) directly modulate the catalytic efficacy. In addition, we reveal that the metal ions have a long-range (~10 Å) electrostatic effect on restructuring water network in the active site. Our study provides evidence that the metal ions in metalloenzymes have a crucial impact on the catalytic mechanism beyond their primary chemical properties.

Imidazole catalyzed silica synthesis: Progress toward understanding the role of histidine in (bio)silicification

2009 ◽  
Vol 24 (5) ◽  
pp. 1700-1708 ◽  
Author(s):  
Mei-Keat Liang ◽  
Siddharth V. Patwardhan ◽  
Elena N. Danilovtseva ◽  
Vadim V. Annenkov ◽  
Carole C. Perry
Keyword(s):  
Molecular Weight ◽  
Silicic Acid ◽  
Catalytic Mechanism ◽  
Synthetic Polymers ◽  
Precipitation Process ◽  
Silica Precipitation ◽  
Silica Synthesis ◽  
Different Molecular Weight

Histidine is an amino acid present in proteins involved in biosilica formation and often found in peptides identified during phage display studies but its role(s) and the extent of its involvement in the silica precipitation process is not fully understood. In this contribution we describe results from an in vitro silicification study conducted using poly-histidine (P-His) and a series of different molecular weight synthetic polymers containing the imidazole functionality (polyvinylimidazole, PVI) for comparison. We show that the presence of imidazole from PVI or P-His is able to catalyze silicic acid condensation; the effect being greater for P-His. The catalytic mechanism is proposed to involve the dual features of the imidazole group—its ability to form hydrogen bonds with silicic acid and electrostatic attraction toward oligomeric silicic acid species.

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