Literature DB >> 15165895

Conformational change in substrate binding, catalysis and product release: an open and shut case?

Alex Gutteridge1, Janet Thornton.   

Abstract

The role of conformational change in substrate binding, catalysis and product release is reviewed for 11 enzymes, for which crystal structures are available for the apo, substrate- and product-bound states. The extent of global conformational changes is measured, and the movements of the functional regions involved in catalysis and ligand binding are compared to the rest of the structure. We find that most of these enzymes undergo relatively small amounts of conformational change and particularly small changes in catalytic residue geometry, usually less than 1 A. In some enzymes there is significant movement of the binding residues, usually on surface loops.

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Year:  2004        PMID: 15165895     DOI: 10.1016/j.febslet.2004.03.067

Source DB:  PubMed          Journal:  FEBS Lett        ISSN: 0014-5793            Impact factor:   4.124


  20 in total

1.  Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates.

Authors:  Hugo Guterres; Hui Sun Lee; Wonpil Im
Journal:  J Chem Theory Comput       Date:  2019-10-14       Impact factor: 6.006

2.  A functional feature analysis on diverse protein-protein interactions: application for the prediction of binding affinity.

Authors:  Jiesi Luo; Yanzhi Guo; Yun Zhong; Duo Ma; Wenling Li; Menglong Li
Journal:  J Comput Aided Mol Des       Date:  2014-05-01       Impact factor: 3.686

3.  Opposites Attract: Escherichia coli Heptosyltransferase I Conformational Changes Induced by Interactions between the Substrate and Positively Charged Residues.

Authors:  Joy M Cote; Cody J S Hecht; Kaelan R Patel; Carlos A Ramirez-Mondragon; Yuk Y Sham; Erika A Taylor
Journal:  Biochemistry       Date:  2020-02-10       Impact factor: 3.162

Review 4.  Molecular pathways for antigenic peptide generation by ER aminopeptidase 1.

Authors:  Anastasia Mpakali; Zachary Maben; Lawrence J Stern; Efstratios Stratikos
Journal:  Mol Immunol       Date:  2018-04-17       Impact factor: 4.407

Review 5.  Capturing the geometry, function, and evolution of enzymes with 3D templates.

Authors:  Ioannis G Riziotis; Janet M Thornton
Journal:  Protein Sci       Date:  2022-07       Impact factor: 6.993

6.  Conformational changes involving ammonia tunnel formation and allosteric control in GMP synthetase.

Authors:  Justin C Oliver; Ravidra Gudihal; John W Burgner; Anthony M Pedley; Alexander T Zwierko; V Jo Davisson; Rebecca S Linger
Journal:  Arch Biochem Biophys       Date:  2014-01-13       Impact factor: 4.013

7.  Halogen Bonding Interactions of Polychlorinated Biphenyls and the Potential for Thyroid Disruption.

Authors:  Eric S Marsan; Craig A Bayse
Journal:  Chemistry       Date:  2020-02-25       Impact factor: 5.236

8.  PSCDB: a database for protein structural change upon ligand binding.

Authors:  Takayuki Amemiya; Ryotaro Koike; Akinori Kidera; Motonori Ota
Journal:  Nucleic Acids Res       Date:  2011-11-10       Impact factor: 16.971

9.  Structure of the T109S mutant of Escherichia coli dihydroorotase complexed with the inhibitor 5-fluoroorotate: catalytic activity is reflected by the crystal form.

Authors:  Mihwa Lee; Megan J Maher; J Mitchell Guss
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2007-02-13

10.  Ligand-Induced Variations in Structural and Dynamical Properties Within an Enzyme Superfamily.

Authors:  Chitra Narayanan; David N Bernard; Khushboo Bafna; Donald Gagné; Pratul K Agarwal; Nicolas Doucet
Journal:  Front Mol Biosci       Date:  2018-06-12
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