Literature DB >> 33190496

Computational Investigation of the Mechanism of Diels-Alderase PyrI4.

Yike Zou1, Song Yang1, Jacob N Sanders1, Wei Li1, Peiyuan Yu1, Hongbo Wang2, Zhijun Tang2, Wen Liu2, K N Houk1.   

Abstract

We studied the mechanisms of activation and stereoselectivity of a monofunctional Diels-Alderase (PyrI4)-catalyzed intramolecular Diels-Alder reaction that leads to formation of the key spiro-tetramate moiety in the biosynthesis of the pyrroindomycin family of natural products. Key activation effects of PyrI4 include acid catalysis and an induced-fit mechanism that cooperate with the unique "lid" feature of PyrI4 to stabilize the Diels-Alder transition state. PyrI4 enhances the intrinsic Diels-Alder stereoselectivity of the substrate and leads to stereospecific formation of the product.

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Year:  2020        PMID： 33190496      PMCID： PMC9328771          DOI： 10.1021/jacs.0c10813

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN： 0002-7863            Impact factor:   16.383


  34 in total

1.  Catalysis on the coastline: theozyme, molecular dynamics, and free energy perturbation analysis of antibody 21D8 catalysis of the decarboxylation of 5-nitro-3-carboxybenzisoxazole.

Authors:  Gregori Ujaque; Dean J Tantillo; Yunfeng Hu; K N Houk; Kinya Hotta; Donald Hilvert
Journal:  J Comput Chem       Date:  2003-01-15       Impact factor: 3.376

2.  Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.

Authors:  Justin B Siegel; Alexandre Zanghellini; Helena M Lovick; Gert Kiss; Abigail R Lambert; Jennifer L St Clair; Jasmine L Gallaher; Donald Hilvert; Michael H Gelb; Barry L Stoddard; Kendall N Houk; Forrest E Michael; David Baker
Journal:  Science       Date:  2010-07-16       Impact factor: 47.728

3.  Structural Insights into a Flavin-Dependent [4 + 2] Cyclase that Catalyzes trans-Decalin Formation in Pyrroindomycin Biosynthesis.

Authors:  Qingfei Zheng; Yukang Gong; Yujiao Guo; Zhixiong Zhao; Zhuhua Wu; Zixuan Zhou; Dandan Chen; Lifeng Pan; Wen Liu
Journal:  Cell Chem Biol       Date:  2018-04-12       Impact factor: 8.116

Review 4.  Theozymes and compuzymes: theoretical models for biological catalysis.

Authors:  D J Tantillo; J Chen; K N Houk
Journal:  Curr Opin Chem Biol       Date:  1998-12       Impact factor: 8.822

5.  Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations.

Authors:  Fabian Paul; Frank Noé; Thomas R Weikl
Journal:  J Phys Chem B       Date:  2018-03-27       Impact factor: 2.991

Review 6.  The expanding world of biosynthetic pericyclases: cooperation of experiment and theory for discovery.

Authors:  Cooper S Jamieson; Masao Ohashi; Fang Liu; Yi Tang; K N Houk
Journal:  Nat Prod Rep       Date:  2019-05-22       Impact factor: 13.423

7.  Control of the exo and endo pathways of the Diels-Alder reaction by antibody catalysis.

Authors:  V E Gouverneur; K N Houk; B de Pascual-Teresa; B Beno; K D Janda; R A Lerner
Journal:  Science       Date:  1993-10-08       Impact factor: 47.728

8.  An antibody exo Diels-Alderase inhibitor complex at 1.95 angstrom resolution.

Authors:  A Heine; E A Stura; J T Yli-Kauhaluoma; C Gao; Q Deng; B R Beno; K N Houk; K D Janda; I A Wilson
Journal:  Science       Date:  1998-03-20       Impact factor: 47.728

9.  Influence of water and enzyme SpnF on the dynamics and energetics of the ambimodal [6+4]/[4+2] cycloaddition.

Authors:  Zhongyue Yang; Song Yang; Peiyuan Yu; Yanwei Li; Charles Doubleday; Jiyong Park; Ashay Patel; Byung-Sun Jeon; William K Russell; Hung-Wen Liu; David H Russell; Kendall N Houk
Journal:  Proc Natl Acad Sci U S A       Date:  2018-01-18       Impact factor: 11.205

Review 10.  The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.

Authors:  Samuel Genheden; Ulf Ryde
Journal:  Expert Opin Drug Discov       Date:  2015-04-02       Impact factor: 6.098
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  1 in total

1.  Mechanism of the Stereoselective Catalysis of Diels-Alderase PyrE3 Involved in Pyrroindomycin Biosynthesis.

Authors:  Bo Li; Xingyi Guan; Song Yang; Yike Zou; Wen Liu; K N Houk
Journal:  J Am Chem Soc       Date:  2022-03-08       Impact factor: 16.383
  1 in total

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