title: Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase.
abstract: Dynamics is a key feature of enzyme catalysis. Unfortunately, current experimental and computational techniques do not yet provide a comprehensive understanding and description of functional macromolecular motions. In this work, we have extended a novel computational technique, which combines molecular modeling methods and robotics algorithms, to investigate functional motions of protein loops. This new approach has been applied to study the functional importance of the so-called thumb-loop in the glycoside hydrolase family 11 xylanase from Thermobacillus xylanilyticus (Tx-xyl). The results obtained provide new insight into the role of the loop in the glycosylation/deglycosylation catalytic cycle, and underline the key importance of the nature of the residue located at the tip of the thumb-loop. The effect of mutations predicted in silico has been validated by in vitro site-directed mutagenesis experiments. Overall, we propose a comprehensive model of Tx-xyl catalysis in terms of substrate and product dynamics by identifying the action of the thumb-loop motion during catalysis.
authors.affiliation: CNRS, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France ; University of Nantes, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France ; INRA, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France ; University of Reims Champagne-Ardenne, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Paës
authors.affiliation: CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France ; University of Toulouse, LAAS, F-31400 Toulouse, France.
authors.forename: Juan
authors.initials: J
authors.lastname: Cortés
authors.affiliation: CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France ; University of Toulouse, LAAS, F-31400 Toulouse, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Siméon
authors.affiliation: INRA, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France ; University of Reims Champagne-Ardenne, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France ; INRA, UMR792 LISBP, 137 avenue de Rangueil, F-31077 Toulouse, France ; INSA, UMR792 LISBP, 137 avenue de Rangueil, F-31077 Toulouse, France.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: O'Donohue
authors.affiliation: CNRS, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France ; University of Nantes, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France.
authors.forename: Vinh
authors.initials: V
authors.lastname: Tran
keywords: Structure-function relationship; molecular modeling; path planning algorithms; xylanase thumb-loop