Literature DB >> 25986631

The Classification and Evolution of Enzyme Function.

Sergio Martínez Cuesta1, Syed Asad Rahman1, Nicholas Furnham2, Janet M Thornton3.   

Abstract

Enzymes are the proteins responsible for the catalysis of life. Enzymes sharing a common ancestor as defined by sequence and structure similarity are grouped into families and superfamilies. The molecular function of enzymes is defined as their ability to catalyze biochemical reactions; it is manually classified by the Enzyme Commission and robust approaches to quantitatively compare catalytic reactions are just beginning to appear. Here, we present an overview of studies at the interface of the evolution and function of enzymes.
Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2015        PMID: 25986631      PMCID: PMC4576142          DOI: 10.1016/j.bpj.2015.04.020

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  51 in total

Review 1.  Toward a systems biology perspective on enzyme evolution.

Authors:  Shelley D Copley
Journal:  J Biol Chem       Date:  2011-11-08       Impact factor: 5.157

Review 2.  Evolution of enzyme superfamilies.

Authors:  Margaret E Glasner; John A Gerlt; Patricia C Babbitt
Journal:  Curr Opin Chem Biol       Date:  2006-08-28       Impact factor: 8.822

Review 3.  Flexibility and reactivity in promiscuous enzymes.

Authors:  Pietro Gatti-Lafranconi; Florian Hollfelder
Journal:  Chembiochem       Date:  2013-01-29       Impact factor: 3.164

Review 4.  Functional and evolutionary implications of gene orthology.

Authors:  Toni Gabaldón; Eugene V Koonin
Journal:  Nat Rev Genet       Date:  2013-04-04       Impact factor: 53.242

5.  New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.

Authors:  Ian Sillitoe; Alison L Cuff; Benoit H Dessailly; Natalie L Dawson; Nicholas Furnham; David Lee; Jonathan G Lees; Tony E Lewis; Romain A Studer; Robert Rentzsch; Corin Yeats; Janet M Thornton; Christine A Orengo
Journal:  Nucleic Acids Res       Date:  2012-11-29       Impact factor: 16.971

6.  Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.

Authors:  Nicholas Furnham; Ian Sillitoe; Gemma L Holliday; Alison L Cuff; Roman A Laskowski; Christine A Orengo; Janet M Thornton
Journal:  PLoS Comput Biol       Date:  2012-03-01       Impact factor: 4.475

7.  The Pfam protein families database.

Authors:  Marco Punta; Penny C Coggill; Ruth Y Eberhardt; Jaina Mistry; John Tate; Chris Boursnell; Ningze Pang; Kristoffer Forslund; Goran Ceric; Jody Clements; Andreas Heger; Liisa Holm; Erik L L Sonnhammer; Sean R Eddy; Alex Bateman; Robert D Finn
Journal:  Nucleic Acids Res       Date:  2011-11-29       Impact factor: 16.971

Review 8.  Enzyme recruitment and its role in metabolic expansion.

Authors:  Cindy Schulenburg; Brian G Miller
Journal:  Biochemistry       Date:  2014-01-31       Impact factor: 3.162

9.  Functional site plasticity in domain superfamilies.

Authors:  Benoit H Dessailly; Natalie L Dawson; Kenji Mizuguchi; Christine A Orengo
Journal:  Biochim Biophys Acta       Date:  2013-03-14

Review 10.  The evolution of enzyme function in the isomerases.

Authors:  Sergio Martinez Cuesta; Nicholas Furnham; Syed Asad Rahman; Ian Sillitoe; Janet M Thornton
Journal:  Curr Opin Struct Biol       Date:  2014-07-05       Impact factor: 6.809

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  19 in total

Review 1.  Tailoring Proteins to Re-Evolve Nature: A Short Review.

Authors:  Angelica Jimenez-Rosales; Miriam V Flores-Merino
Journal:  Mol Biotechnol       Date:  2018-12       Impact factor: 2.695

Review 2.  Using Evolution to Guide Protein Engineering: The Devil IS in the Details.

Authors:  Liskin Swint-Kruse
Journal:  Biophys J       Date:  2016-07-12       Impact factor: 4.033

3.  To what extent do structural changes in catalytic metal sites affect enzyme function?

Authors:  Yana Valasatava; Antonio Rosato; Nicholas Furnham; Janet M Thornton; Claudia Andreini
Journal:  J Inorg Biochem       Date:  2017-11-08       Impact factor: 4.155

4.  Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family.

Authors:  Martin Marek; Radka Chaloupkova; Tatyana Prudnikova; Yukari Sato; Pavlina Rezacova; Yuji Nagata; Ivana Kuta Smatanova; Jiri Damborsky
Journal:  Comput Struct Biotechnol J       Date:  2020-06-03       Impact factor: 7.271

Review 5.  Melting Down Protein Stability: PAPS Synthase 2 in Patients and in a Cellular Environment.

Authors:  Oliver Brylski; Simon Ebbinghaus; Jonathan W Mueller
Journal:  Front Mol Biosci       Date:  2019-05-03

6.  COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.

Authors:  Yi-Chien Chang; Zhenjun Hu; John Rachlin; Brian P Anton; Simon Kasif; Richard J Roberts; Martin Steffen
Journal:  Nucleic Acids Res       Date:  2015-12-03       Impact factor: 16.971

7.  Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases.

Authors:  Maria Laura Mascotti; Maximiliano Juri Ayub; Nicholas Furnham; Janet M Thornton; Roman A Laskowski
Journal:  J Mol Biol       Date:  2016-07-14       Impact factor: 5.469

8.  A computational method for prediction of xylanase enzymes activity in strains of Bacillus subtilis based on pseudo amino acid composition features.

Authors:  Shohreh Ariaeenejad; Maryam Mousivand; Parinaz Moradi Dezfouli; Maryam Hashemi; Kaveh Kavousi; Ghasem Hosseini Salekdeh
Journal:  PLoS One       Date:  2018-10-22       Impact factor: 3.240

9.  Fatty acid based transient nanostructures for temporal regulation of artificial peroxidase activity.

Authors:  Sahnawaz Ahmed; Ayan Chatterjee; Krishnendu Das; Dibyendu Das
Journal:  Chem Sci       Date:  2019-07-01       Impact factor: 9.825

10.  Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation.

Authors:  Nandini Sharma; Navjeet Ahalawat; Padmani Sandhu; Erick Strauss; Jagannath Mondal; Ruchi Anand
Journal:  Sci Adv       Date:  2020-04-03       Impact factor: 14.136

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