The Crystal Structure of RosB: Insights into the Reaction Mechanism of the First Member of a Family of Flavodoxin-like Enzymes

2016 ◽  
Vol 56 (4) ◽  
pp. 1146-1151 ◽  
Author(s):  
Valentino Konjik ◽  
Steffen Brünle ◽  
Ulrike Demmer ◽  
Amanda Vanselow ◽  
Roger Sandhoff ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Reaction Mechanism

The crystal structure of human mitochondrial 3-ketoacyl-CoA thiolase (T1): insight into the reaction mechanism of its thiolase and thioesterase activities

2014 ◽  
Vol 70 (12) ◽  
pp. 3212-3225 ◽  
Author(s):  
Tiila-Riikka Kiema ◽  
Rajesh K. Harijan ◽  
Malgorzata Strozyk ◽  
Toshiyuki Fukao ◽  
Stefan E. H. Alexson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Reaction Mechanism ◽  
Active Site ◽  
Quaternary Structure ◽  
Fatty Acyl ◽  
Physiological Importance ◽  
Loop Domain ◽  
Solution Studies ◽  
Hydrolysis Of ◽  
Insight Into

Crystal structures of human mitochondrial 3-ketoacyl-CoA thiolase (hT1) in the apo form and in complex with CoA have been determined at 2.0 Å resolution. The structures confirm the tetrameric quaternary structure of this degradative thiolase. The active site is surprisingly similar to the active site of theZoogloea ramigerabiosynthetic tetrameric thiolase (PDB entries 1dm3 and 1m1o) and different from the active site of the peroxisomal dimeric degradative thiolase (PDB entries 1afw and 2iik). A cavity analysis suggests a mode of binding for the fatty-acyl tail in a tunnel lined by the Nβ2–Nα2 loop of the adjacent subunit and the Lα1 helix of the loop domain. Soaking of the apo hT1 crystals with octanoyl-CoA resulted in a crystal structure in complex with CoA owing to the intrinsic acyl-CoA thioesterase activity of hT1. Solution studies confirm that hT1 has low acyl-CoA thioesterase activity for fatty acyl-CoA substrates. The fastest rate is observed for the hydrolysis of butyryl-CoA. It is also shown that T1 has significant biosynthetic thiolase activity, which is predicted to be of physiological importance.

scholarly journals Crystal structure of the yeast His6 enzyme suggests a reaction mechanism

2006 ◽  
Vol 15 (6) ◽  
pp. 1516-1521 ◽  
Author(s):  
Sophie Quevillon-Cheruel ◽  
Nicolas Leulliot ◽  
Marc Graille ◽  
Karine Blondeau ◽  
Joel Janin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Reaction Mechanism

scholarly journals The metal centres of particulate methane mono-oxygenase

2008 ◽  
Vol 36 (6) ◽  
pp. 1134-1137 ◽  
Author(s):  
Amy C. Rosenzweig
Keyword(s):  
Crystal Structure ◽  
Reaction Mechanism ◽  
Structure Determination ◽  
Active Site ◽  
Spectroscopic Data ◽  
Present Review ◽  
Methylococcus Capsulatus ◽  
Research Groups ◽  
Oxidation Of Methane ◽  
Before And After

pMMO (particulate methane mono-oxygenase) is an integral membrane metalloenzyme that catalyses the oxidation of methane to methanol. The pMMO metal active site has not been identified, precluding detailed investigation of the reaction mechanism. Models for the metal centres proposed by various research groups have evolved as crystallographic and spectroscopic data have become available. The present review traces the evolution of these active-site models before and after the 2005 Methylococcus capsulatus (Bath) pMMO crystal structure determination.

scholarly journals 2P060 Crystal structure of TilS : implications for reaction mechanism

2004 ◽  
Vol 44 (supplement) ◽  
pp. S124
Author(s):  
K. Nakanishi ◽  
S. Fukai ◽  
Y. Ikeuchi ◽  
A. Soma ◽  
T. Suzuki ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Reaction Mechanism

Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP

2020 ◽  
Vol 168 (3) ◽  
pp. 223-229
Author(s):  
Yoshinori Shibanuma ◽  
Naoki Nemoto ◽  
Norifumi Yamamoto ◽  
Gen-Ichi Sampei ◽  
Gota Kawai
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Adenylate Kinase ◽  
Reaction Coordinate ◽  
Amino Acid Residues ◽  
Aeropyrum Pernix ◽  
Adenylate Kinases

Abstract The crystal structure of an adenylate kinase from an extremophilic archaeon Aeropyrum pernix was determined in complex with full ligands, ATP-Mg2+ and AMP, at a resolution of 2.0 Å. The protein forms a trimer as found for other adenylate kinases from archaea. Interestingly, the reacting three atoms, two phosphorus and one oxygen atoms, were located almost in line, supporting the SN2 nucleophilic substitution reaction mechanism. Based on the crystal structure obtained, the reaction coordinate was estimated by the quantum mechanics calculations combined with molecular dynamics. It was found that the reaction undergoes two energy barriers; the steps for breaking the bond between the oxygen and γ-phosphorus atoms of ATP to produce a phosphoryl fragment and creating the bond between the phosphoryl fragment and the oxygen atom of the β-phosphate group of ADP. The reaction coordinate analysis also suggested the role of amino-acid residues for the catalysis of adenylate kinase.

scholarly journals Reaction mechanism of tetrathionate hydrolysis based on the crystal structure of tetrathionate hydrolase from Acidithiobacillus ferrooxidans

2020 ◽  
Vol 30 (2) ◽  
pp. 328-338
Author(s):  
Tadayoshi Kanao ◽  
Naruki Hase ◽  
Hisayuki Nakayama ◽  
Kyoya Yoshida ◽  
Kazumi Nishiura ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Reaction Mechanism ◽  
Acidithiobacillus Ferrooxidans

1,3-Dipolar [3+3] Cycloaddition of 1,4-Benzodiazepinone-Based Nitrones with α-Halohydroxamates for Diastereoselective Synthesis of Novel d-Edge Heterocycle-Fused 1,4-Benzodiazepinones

Synlett ◽  
2021 ◽  
Author(s):  
Hong-Wu Zhao ◽  
Heng Zhang ◽  
Lu-Yu Cai ◽  
Zhe Tang ◽  
Xiao-Zu Fan ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Reaction Mechanism ◽  
Single Crystal ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
Diastereoselective Synthesis ◽  
Reaction Conditions ◽  
Relative Configuration ◽  
X Ray ◽  
Single Crystal Structure Analysis

Promoted by K2CO3 (2.0 equiv), the 1,3-dipolar [3+3] cycloaddition between 1, 4-benzodiazepinone-based nitrones and α-halohydroxamates processed smoothly under the mild reaction conditions and delivered structurally novel and complex cis or trans-configured d-edge-heterocycle-fused 1,4-benzodiazepinones in up to >99% isolated yield with >20:1 dr. The relative configuration of the title chemical entities was clearly identified with the use of X-ray single crystal structure analysis. The reaction mechanism was assumed to interpret the diastereoselective production of the obtained cis or trans-configured d-edge-heterocycle-fused 1, 4-benzodiazepinones.

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