Hydrogen Bonding at the Active Site of Δ5-3-Ketosteroid Isomerase†

AbstractWe demonstrate how a full QM/MM derivatization of the recently developed GOCAT model can be utilized in the global optimization of molecular embeddings. To this end, we provide two distinct examples: An $$\text {S}_\text {N}2$$ S N 2 reaction, and one enzymatic example of recent interest, the ketosteroid isomerase. These serve us to highlight the advantages of such an approach and sketch the roadmap for further improvements.

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

Nature Communications ◽

10.1038/s41467-021-22626-x ◽

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.

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

10.26434/chemrxiv.7756214 ◽

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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A crystallographic study of the Toho-1 β-lactamase acylation mechanism

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314087920 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1207-C1207

Author(s):

Leighton Coates

Keyword(s):

Hydrogen Bonding ◽

Transition State ◽

Active Site ◽

Catalytic Mechanism ◽

Substrate Binding ◽

Ligand Complex ◽

Transition State Analog ◽

Hydrogen Bonding Interactions ◽

Active Site Region ◽

Neutron Crystallography

β-lactam antibiotics have been used effectively over several decades against many types of highly virulent bacteria. The predominant cause of resistance to these antibiotics in Gram-negative bacterial pathogens is the production of serine β-lactamase enzymes. A key aspect of the class A serine β-lactamase mechanism that remains unresolved and controversial is the identity of the residue acting as the catalytic base during the acylation reaction. Multiple mechanisms have been proposed for the formation of the acyl-enzyme intermediate that are predicated on understanding the protonation states and hydrogen-bonding interactions among the important residues involved in substrate binding and catalysis of these enzymes. For resolving a controversy of this nature surrounding the catalytic mechanism, neutron crystallography is a powerful complement to X-ray crystallography that can explicitly determine the location of deuterium atoms in proteins, thereby directly revealing the hydrogen-bonding interactions of important amino acid residues. Neutron crystallography was used to unambiguously reveal the ground-state active site protonation states and the resulting hydrogen-bonding network in two ligand-free Toho-1 β-lactamase mutants which provided remarkably clear pictures of the active site region prior to substrate binding and subsequent acylation [1,2] and an acylation transition-state analog, benzothiophene-2-boronic acid (BZB), which was also isotopically enriched with 11B. The neutron structure revealed the locations of all deuterium atoms in the active site region and clearly indicated that Glu166 is protonated in the BZB transition-state analog complex. As a result, the complete hydrogen-bonding pathway throughout the active site region could then deduced for this protein-ligand complex that mimics the acylation tetrahedral intermediate [3].

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