scholarly journals The first crystal structure of human RNase 6 reveals a novel substrate-binding and cleavage site arrangement

2016 ◽  
Vol 473 (11) ◽  
pp. 1523-1536 ◽  
Author(s):  
Guillem Prats-Ejarque ◽  
Javier Arranz-Trullén ◽  
Jose A. Blanco ◽  
David Pulido ◽  
M. Victòria Nogués ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Kinetic Analysis ◽  
Cleavage Site ◽  
Substrate Recognition ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Cleavage Sites ◽  
Human Rnase ◽  
Dynamics Simulations

We describe the first human RNase 6 crystal structure in complex with sulfate anions. Kinetic analysis, site-directed mutagenesis and molecular dynamics simulations identified novel substrate recognition and cleavage sites.

scholarly journals Identification of key binding site residues of MCT1 for AR-C155858 reveals the molecular basis of its isoform selectivity

2015 ◽  
Vol 466 (1) ◽  
pp. 177-188 ◽  
Author(s):  
Bethany Nancolas ◽  
Richard B. Sessions ◽  
Andrew P. Halestrap
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Binding Site ◽  
Molecular Basis ◽  
Specific Inhibitor ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Isoform Specificity ◽  
Isoform Selectivity ◽  
Dynamics Simulations

A combination of molecular modelling, site-directed mutagenesis and molecular dynamics simulations define the binding site of MCT1 for AR-C155858, a potent and specific inhibitor. Key amino acids within the binding site differ between MCT1 and MCT4 accounting for isoform specificity.

scholarly journals Increasing the thermostability of the neutral proteinase of Bacillus stearothermophilus by improvement of internal hydrogen-bonding

1992 ◽  
Vol 285 (2) ◽  
pp. 625-628 ◽  
Author(s):  
V G Eijsink ◽  
G Vriend ◽  
J R Van der Zee ◽  
B Van den Burg ◽  
G Venema
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Bacillus Stearothermophilus ◽  
Site Directed Mutagenesis ◽  
Internal Cavity ◽  
Directed Mutagenesis ◽  
Neutral Proteinase ◽  
Internal Hydrogen ◽  
Internal Hydrogen Bond ◽  
Dynamics Simulations

In an attempt to increase the thermostability of the neutral proteinase of Bacillus stearothermophilus the buried Ala-170 was replaced by serine. Molecular-dynamics simulations showed that Ser-170 stabilizes the enzyme by formation of an internal hydrogen bond. In addition, the hydroxy group of Ser-170 could contribute to stability by filling an internal cavity. After the introduction of the mutation, using site-directed-mutagenesis techniques, an increase in stability of 0.7 +/- 0.1 degrees C was obtained.

Structural and biochemical analyses of theStreptococcus pneumoniaeL,D-carboxypeptidase DacB

2015 ◽  
Vol 71 (2) ◽  
pp. 283-292
Author(s):  
Juan Zhang ◽  
Yi-Hu Yang ◽  
Yong-Liang Jiang ◽  
Cong-Zhao Zhou ◽  
Yuxing Chen
Keyword(s):  
Crystal Structure ◽  
Molecular Docking ◽  
Catalytic Mechanism ◽  
Substrate Recognition ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Binding Properties ◽  
Biochemical Analyses ◽  
Key Residues ◽  
Structural Insights

The L,D-carboxypeptidase DacB plays a key role in the remodelling ofStreptococcus pneumoniaepeptidoglycan during cell division. In order to decipher its substrate-binding properties and catalytic mechanism, the 1.71 Å resolution crystal structure of DacB fromS. pneumoniaeTIGR4 is reported. Structural analyses in combination with comparisons with the recently reported structures of DacB fromS. pneumoniaeD39 and R6 clearly demonstrate that DacB adopts a zinc-dependent carboxypeptidase fold and belongs to the metallopeptidase M15B subfamily. In addition, enzymatic activity assays further confirm that DacB indeed acts as an L,D-carboxypeptidase towards the tetrapeptide L-Ala-D-iGln-L-Lys-D-Ala of the peptidoglycan stem, withKmandkcatvalues of 2.84 ± 0.37 mMand 91.49 ± 0.05 s−1, respectively. Subsequent molecular docking and site-directed mutagenesis enable the assignment of the key residues that bind to the tetrapeptide. Altogether, these findings provide structural insights into substrate recognition in the metallopeptidase M15B subfamily.

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