Structural Analysis of 1-Aminocyclopropane-1-Carboxylate Deaminase: Observation of an Aminyl Intermediate and Identification of Tyr 294 as the Active-Site Nucleophile

2004 ◽  
Vol 116 (26) ◽  
pp. 3507-3511
Author(s):  
Subramanian Karthikeyan ◽  
Zongbao Zhao ◽  
Chai-lin Kao ◽  
Qingxian Zhou ◽  
Zhihua Tao ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Active Site

Kinetic and Structural Analysis of Active Site Mutants of Monofunctional NAD-Dependent 5,10-Methylenetetrahydrofolate Dehydrogenase fromSaccharomyces cerevisiae†

Biochemistry ◽  
2005 ◽  
Vol 44 (39) ◽  
pp. 13163-13171 ◽  
Author(s):  
Wendi Wagner ◽  
Andrew P. Breksa ◽  
Arthur F. Monzingo ◽  
Dean R. Appling ◽  
Jon D. Robertus
Keyword(s):  
Structural Analysis ◽  
Active Site ◽  
Methylenetetrahydrofolate Dehydrogenase ◽  
Active Site Mutants

scholarly journals A structural analysis of the group II intron active site and implications for the spliceosome

RNA ◽  
2009 ◽  
Vol 16 (1) ◽  
pp. 1-9 ◽  
Author(s):  
K. S. Keating ◽  
N. Toor ◽  
P. S. Perlman ◽  
A. M. Pyle
Keyword(s):  
Structural Analysis ◽  
Active Site ◽  
Group Ii Intron ◽  
Group Ii

Structural insights into the peroxidase activity and inactivation of human peroxiredoxin 4

2011 ◽  
Vol 441 (1) ◽  
pp. 113-118 ◽  
Author(s):  
Xi Wang ◽  
Likun Wang ◽  
Xi'e Wang ◽  
Fei Sun ◽  
Chih-chen Wang
Keyword(s):  
Endoplasmic Reticulum ◽  
Structural Analysis ◽  
Conformational Changes ◽  
Active Site ◽  
High Reactivity ◽  
Structural Explanation ◽  
Disulfide Formation ◽  
Redox Forms ◽  
Structural Insights

Prx4 (peroxiredoxin 4) is the only peroxiredoxin located in the ER (endoplasmic reticulum) and a proposed scavenger for H2O2. In the present study, we solved crystal structures of human Prx4 in three different redox forms and characterized the reaction features of Prx4 with H2O2. Prx4 exhibits a toroid-shaped decamer constructed of five catalytic dimers. Structural analysis revealed conformational changes around helix α2 and the C-terminal reigon with a YF (Tyr-Phe) motif from the partner subunit, which are required for interchain disulfide formation between Cys87 and Cys208, a critical step of the catalysis. The structural explanation for the restricting role of the YF motif on the active site dynamics is provided in detail. Prx4 has a high reactivity with H2O2, but is susceptible to overoxidation and consequent inactivation by H2O2. Either deletion of the YF motif or dissociation into dimers decreased the susceptibility of Prx4 to overoxidation by increasing the flexibility of Cys87.

Structural analysis of the inhibition of thermolysin by an active-site-directed irreversible inhibitor

Biochemistry ◽  
1983 ◽  
Vol 22 (1) ◽  
pp. 236-240 ◽  
Author(s):  
M. A. Holmes ◽  
D. E. Tronrud ◽  
B. W. Matthews
Keyword(s):  
Structural Analysis ◽  
Active Site ◽  
Irreversible Inhibitor

scholarly journals The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 5053
Author(s):  
Alina K. Bakunova ◽  
Alena Yu. Nikolaeva ◽  
Tatiana V. Rakitina ◽  
Tatiana Y. Isaikina ◽  
Maria G. Khrenova ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Structural Analysis ◽  
Active Site ◽  
Active Sites ◽  
Structural Basis ◽  
Active Site Residues ◽  
Type Iv ◽  
Fold Type ◽  
Arginine Residues

Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.

scholarly journals Multi-active Site Dynamics on a Molecular Cr/Co/Se Cluster Catalyst

2022 ◽  
Author(s):  
Jonathan Kephart ◽  
Benjamin Mitchell ◽  
Werner Kaminsky ◽  
Alexandra Velian
Keyword(s):  
Structural Analysis ◽  
Active Site ◽  
Resting State ◽  
Active Sites ◽  
Stepwise Mechanism ◽  
Nitrene Transfer ◽  
Catalytic Intermediates ◽  
Edge Site ◽  
Catalytically Active

This study provides detailed insights into the interconnected reactivity of the three catalytically active sites of an atomically precise nanocluster Cr3(py)3Co6Se8L6 (Cr3(py)3, L = Ph2PNTol–, Ph = phenyl, Tol = 4-tolyl). Catalytic and stoichiometric studies into tosyl azide activation and carbodiimide formation enabled the isolation and crystallographic characterization of key metal-nitrenoid catalytic intermediates, including the tris(nitrenoid) cluster Cr3(NTs)3, the catalytic resting state Cr3(NTs)3(CNtBu)3, and the mono(nitrenoid) cluster Cr3(NTs)(CNtBu)2. Nitrene transfer proceeds via a stepwise mechanism, with the three active sites engaging sequentially to produce carbodiimide. Comparative structural analysis and CNtBu bind-ing studies reveal that the chemical state of neighboring active sites regulates the affinity for substrates of an individual Cr-nitrenoid edge site, intertwining their reactivity through the inorganic support.

scholarly journals Homology modelling and structural analysis of human arylamine N-acetyltransferase NAT1: evidence for the conservation of a cysteine protease catalytic domain and an active-site loop

2001 ◽  
Vol 356 (2) ◽  
pp. 327 ◽  
Author(s):  
Fernando RODRIGUES-LIMA ◽  
Claudine DELOMÉNIE ◽  
Geoffrey H. GOODFELLOW ◽  
Denis M. GRANT ◽  
Jean-Marie DUPRET
Keyword(s):  
Structural Analysis ◽  
Cysteine Protease ◽  
Active Site ◽  
Catalytic Domain ◽  
Homology Modelling
Sign in / Sign up

Export Citation Format

Share Document