Residue Accessibility, Hydrogen Bonding, and Molecular Recognition:  Metal−Chelate Probing of Active Site Histidines in Chymotrypsins†

Biochemistry ◽  
1997 ◽  
Vol 36 (23) ◽  
pp. 6896-6905 ◽  
Author(s):  
Patrick P. Berna ◽  
Nadir T. Mrabet ◽  
Jozef Van Beeumen ◽  
Bart Devreese ◽  
Jerker Porath ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Recognition ◽  
Active Site ◽  
Metal Chelate

scholarly journals Residue Accessibility, Hydrogen Bonding, and Molecular Recognition:  Metal−Chelate Probing of Active Site Histidines in Chymotrypsins

Biochemistry ◽  
1997 ◽  
Vol 36 (51) ◽  
pp. 16355-16356
Author(s):  
Patrick P. Berna ◽  
Nadir T. Mrabet ◽  
Jozef Van Beeumen ◽  
Bart Devreese ◽  
Jerker Porath ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Recognition ◽  
Active Site ◽  
Metal Chelate

scholarly journals How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dariusz Czernecki ◽  
Pierre Legrand ◽  
Mustafa Tekpinar ◽  
Sandrine Rosario ◽  
Pierre-Alexandre Kaminski ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Active Site ◽  
Metal Ion ◽  
Restriction Endonucleases ◽  
Structural Element

AbstractBacteriophages have long been known to use modified bases in their DNA to prevent cleavage by the host’s restriction endonucleases. Among them, cyanophage S-2L is unique because its genome has all its adenines (A) systematically replaced by 2-aminoadenines (Z). Here, we identify a member of the PrimPol family as the sole possible polymerase of S-2L and we find it can incorporate both A and Z in front of a T. Its crystal structure at 1.5 Å resolution confirms that there is no structural element in the active site that could lead to the rejection of A in front of T. To resolve this contradiction, we show that a nearby gene is a triphosphohydolase specific of dATP (DatZ), that leaves intact all other dNTPs, including dZTP. This explains the absence of A in S-2L genome. Crystal structures of DatZ with various ligands, including one at sub-angstrom resolution, allow to describe its mechanism as a typical two-metal-ion mechanism and to set the stage for its engineering.

Molecular recognition: hydrogen-bonding receptors that function in highly competitive solvents

1993 ◽  
Vol 115 (1) ◽  
pp. 369-370 ◽  
Author(s):  
Erkang Fan ◽  
Scott A. Van Arman ◽  
Scott Kincaid ◽  
Andrew D. Hamilton
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Recognition

scholarly journals The Geometry of the Catalytic Active Site in [FeFe]-Hydrogenases is Determined by Hydrogen Bonding and Proton Transfer

2019 ◽  
Author(s):  
Jifu Duan ◽  
Stefan Mebs ◽  
Moritz Senger ◽  
Konstantin Laun ◽  
Florian Wittkamp ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Active Site ◽  
Time Resolved ◽  
X Ray Crystallography ◽  
Hydrogen Bonding Interactions ◽  
Catalytic Active Site ◽  
Catalytic Intermediates ◽  
Time Resolved Infrared Spectroscopy

The H2 conversion and CO inhibition reactivity of nine [FeFe]-hydrogenase constructs with semi-artificial cofactors was studied by in situ and time-resolved infrared spectroscopy, X-ray crystallography, and theoretical methods. Impaired hydrogen turnover and proton transfer as well as characteristic CO inhibition/ reactivation kinetics are assigned to varying degrees of hydrogen-bonding interactions at the active site. We show that the probability to adopt catalytic intermediates is modulated by intramolecular and protein-cofactor interactions that govern structural dynamics at the active site of [FeFe]-hydrogenases.<br>

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