Molecular basis of the general base catalysis of an α/β-hydrolase catalytic triad.
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TLDR
These findings suggest that the open-closed conformational change tightly couples formation of the catalytic triad to substrate binding to enhance the substrate specificities and simultaneously shield the nucleophilicity of the triad, thus allowing it to expand its catalytic power beyond theucleophilic catalysis.About:
This article is published in Journal of Biological Chemistry.The article was published on 2014-05-30 and is currently open access. It has received 26 citations till now. The article focuses on the topics: Catalytic triad & Enzyme catalysis.read more
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How the Same Core Catalytic Machinery Catalyzes 17 Different Reactions: the Serine-Histidine-Aspartate Catalytic Triad of α/β-Hydrolase Fold Enzymes
TL;DR: Detailed analysis of the subset of α/β-hydrolase fold enzymes that contain the serine-histidine-aspartate catalytic triad shows that binding differences and non-catalytic residues create new mechanisms and are essential for understanding and designing efficient enzymes.
Journal ArticleDOI
Hydrogen Bonds: Simple after All?
TL;DR: The advances that have led to a remarkably simple picture of the structure of hydrogen bonds are recounted, including five "Rules for Hydrogen Bonding" that may provide a foundation for understanding and teaching about these vital interactions and for building toward a deeper understanding of hydrogen bond energetics.
Journal ArticleDOI
The modular structure of α/β-hydrolases
TL;DR: The α/β‐hydrolases were distinguished by their oxyanion hole signature (GX‐, GGGX‐ and Y‐types), and the classification was applied to the newly discovered polyethylene terephthalate (PET)‐degrading PETases and MHETases, which are core domain α/ β‐Hydrolases of the G X‐ and the G GGX‐type respectively.
Journal ArticleDOI
Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein.
Margaux M. Pinney,Aditya Natarajan,Filip Yabukarski,David M. Sanchez,Fang Liu,Ruibin Liang,Tzanko Doukov,Jason P. Schwans,Todd J. Martínez,Daniel Herschlag +9 more
TL;DR: The fundamental questions of whether, and to what extent, hydrogen bonds within networks are structurally coupled are asked, providing strong evidence for long-range coupling and for the extent of this coupling.
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Challenges in biodegradation of non-degradable thermoplastic waste: From environmental impact to operational readiness.
TL;DR: In this article, the advantages and limitations of current plastic degradation methods, their technology readiness levels (TRL), biodegradation mechanisms and the associated challenges in biodegradability are assessed in detail.
References
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Book ChapterDOI
Processing of X-ray diffraction data collected in oscillation mode
Zbyszek Otwinowski,Wladek Minor +1 more
TL;DR: The methods presented in the chapter have been applied to solve a large variety of problems, from inorganic molecules with 5 A unit cell to rotavirus of 700 A diameters crystallized in 700 × 1000 × 1400 A cell.
Journal ArticleDOI
Clustal W and Clustal X version 2.0
Mark A. Larkin,Gordon Blackshields,Nigel P. Brown,R. Chenna,Paul A. McGettigan,Hamish McWilliam,Franck Valentin,Iain M. Wallace,Andreas Wilm,Rodrigo Lopez,J.D. Thompson,Toby J. Gibson,Desmond G. Higgins +12 more
TL;DR: The Clustal W and ClUSTal X multiple sequence alignment programs have been completely rewritten in C++ to facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
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PROCHECK: a program to check the stereochemical quality of protein structures
TL;DR: The PROCHECK suite of programs as mentioned in this paper provides a detailed check on the stereochemistry of a protein structure and provides an assessment of the overall quality of the structure as compared with well refined structures of the same resolution.
Journal ArticleDOI
Features and development of Coot.
TL;DR: Coot is a molecular-graphics program designed to assist in the building of protein and other macromolecular models and the current state of development and available features are presented.