The Molecular Mechanism of Enzymatic Glycosyl Transfer with Retention of Configuration: Evidence for a Short-Lived Oxocarbenium-Like Species

被引:84
作者
Ardevol, Albert [1 ]
Rovira, Carme [1 ,2 ]
机构
[1] Parc Cient Barcelona, Comp Simulat & Modeling Lab CoSMoLAB, Barcelona 08028, Spain
[2] ICREA, Barcelona 08020, Spain
关键词
computational chemistry; glycosides; reaction mechanisms; transferases; transition states; RETAINING GALACTOSYLTRANSFERASE LGTC; DYNAMICS SIMULATIONS; QM/MM METADYNAMICS; GLYCOSYLTRANSFERASES; HYDROLYSIS; INSIGHT; COMPLEX;
D O I
10.1002/anie.201104623
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
A quantum leap: By means of quantum mechanics/molecular mechanics metadynamics simulations, a front-face SNi-type reaction for glycosyl transfer with retention of the anomeric configuration is shown to be feasible. A short-lived oxocarbenium-like species (see picture; O red, P gold, N blue, C black) is identified and provides the complete itinerary of this long sought after molecular mechanism. © 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
引用
收藏
页码:10897 / 10901
页数:5
相关论文
共 29 条
[1]   On the reaction pathways and determination of transition-state structures for retaining α-galactosyltransferases [J].
André, I ;
Tvaroska, I ;
Carver, JP .
CARBOHYDRATE RESEARCH, 2003, 338 (09) :865-877
[2]   Mechanism of Xylobiose Hydrolysis by GH43 β-Xylosidase [J].
Barker, Ian J. ;
Petersen, Luis ;
Reilly, Peter J. .
JOURNAL OF PHYSICAL CHEMISTRY B, 2010, 114 (46) :15389-15393
[3]   Substrate distortion in the michaelis complex of Bacillus 1,3-1,4-β-glucanase -: Insight from first principles molecular dynamics simulations [J].
Biarnés, X ;
Nieto, J ;
Planas, A ;
Rovira, C .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2006, 281 (03) :1432-1441
[4]   Hsc70 ATPase:: An insight into water dissociation and joint catalytic role of K+ and Mg2+ metal cations in the hydrolysis reaction [J].
Boero, Mauro ;
Ikeda, Takashi ;
Ito, Etsuro ;
Terakura, Kiyoyuki .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2006, 128 (51) :16798-16807
[5]   UNIFIED APPROACH FOR MOLECULAR-DYNAMICS AND DENSITY-FUNCTIONAL THEORY [J].
CAR, R ;
PARRINELLO, M .
PHYSICAL REVIEW LETTERS, 1985, 55 (22) :2471-2474
[6]   Mechanistic Insight into Enzymatic Glycosyl Transfer with Retention of Configuration through Analysis of Glycomimetic Inhibitors [J].
Errey, James C. ;
Lee, Seung Seo ;
Gibson, Robert P. ;
Fleites, Carlos Martinez ;
Barry, Conor S. ;
Jung, Pierre M. J. ;
O'Sullivan, Anthony C. ;
Davis, Benjamin G. ;
Davies, Gideon J. .
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2010, 49 (07) :1234-1237
[7]   THE PATH OF CHEMICAL-REACTIONS - THE IRC APPROACH [J].
FUKUI, K .
ACCOUNTS OF CHEMICAL RESEARCH, 1981, 14 (12) :363-368
[8]   Bovine α1,3-galactosyltransferase catalytic domain structure and its relationship with ABO histo-blood group and glycosphingolipid glycosyltransferases [J].
Gastinel, LN ;
Bignon, C ;
Misra, AK ;
Hindsgaul, O ;
Shaper, JH ;
Joziasse, DH .
EMBO JOURNAL, 2001, 20 (04) :638-649
[9]   Sucrose Phosphorylase Harbouring a Redesigned, Glycosyltransferase-Like Active Site Exhibits Retaining Glucosyl Transfer in the Absence of a Covalent Intermediate [J].
Goedl, Christiane ;
Nidetzky, Bernd .
CHEMBIOCHEM, 2009, 10 (14) :2333-2337
[10]   VMD: Visual molecular dynamics [J].
Humphrey, W ;
Dalke, A ;
Schulten, K .
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 1996, 14 (01) :33-38