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Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function

Daniel E. Almonacid, Emmanuel R. Yera, John B. O. Mitchell, Patricia C. Babbitt, Christine A. Orengo
2010 PLoS Computational Biology  
Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of  ...  be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions.  ...  Sunil Ojha for fruitful discussions about enzyme reaction mechanisms and enzyme evolution, and Dr. Gemma Holliday for providing MACiE version 2.3.9 data in RDF format and pictures in CDX format.  ... 
doi:10.1371/journal.pcbi.1000700 pmid:20300652 pmcid:PMC2837397 fatcat:gzf6fvbshzh6xcg5xuxargqs4i

The evolution of enzyme function in the isomerases

Sergio Martinez Cuesta, Nicholas Furnham, Syed Asad Rahman, Ian Sillitoe, Janet M Thornton
2014 Current Opinion in Structural Biology  
themed issue on Sequences and topology Isomerases are present in the metabolism and genome of most living organisms, catalysing up to 4% of the biochemical reactions present in central metabolism, in  ...  This paper reviews research efforts aiming to understand the evolution of enzyme function in superfamilies, presenting a novel strategy to provide an overview of the evolution of enzymes belonging to an  ...  Acknowledgements SMC acknowledges Dr Tjaart de Beer and Dr Roman Laskowski for technical discussions and support from the EMBL International PhD Programme.  ... 
doi:10.1016/j.sbi.2014.06.002 pmid:25000289 pmcid:PMC4139412 fatcat:jl366uxgrfchpdgknr5dl5pehm

Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies

Nicholas Furnham, Natalie L. Dawson, Syed A. Rahman, Janet M. Thornton, Christine A. Orengo
2016 Journal of Molecular Biology  
In others, large changes of enzyme function, in terms of both overall chemistry and substrate specificity, have been brought about by significant changes in catalytic machinery.  ...  Enzymes, as biological catalysts, form the basis of all forms of life. How these proteins have evolved their functions remains a fundamental question in biology.  ...  /products and reaction chemistries from MACiE (Mechanism, Annotation, and Classification in Enzymes) [11] and catalytic residue data from the Catalytic Site Atlas (CSA) [12] .  ... 
doi:10.1016/j.jmb.2015.11.010 pmid:26585402 pmcid:PMC4751976 fatcat:rqkj2aj7nrbhzngzy7q3sppquq

At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Shina C. L. Kamerlin, Arieh Warshel
2010 Proteins: Structure, Function, and Bioinformatics  
Enzymes play a key role in almost all biological processes, accelerating a variety of metabolic reactions as well as controlling energy transduction, transcription and translation of genetic information  ...  Thus, there is broad interest in understanding the catalytic power of enzymes on a molecular level.  ...  Acknowledgments This work was supported by NIH grants GM24492 and 5U19A105010, NSF grant MCB-0342276, and NCI grant 1 U19 1050101-01.  ... 
doi:10.1002/prot.22654 pmid:20099310 pmcid:PMC2841229 fatcat:7bhujoyh2reunehm7ndi3zsbsu

A proficient enzyme

A Radzicka, R Wolfenden
1995 Science  
For k cat and k cat /K M for yeast OMPDC and k cat /K M for the archaeal M. thermautorophicus OMPDC, OMP decarboxylation was found to be only partially dependent on the rate of chemical steps in the enzyme  ...  By applying the tools of enzymology learned in the Gerlt Laboratory and working successfully with numerous collaborators, I have furthered our understanding of the mechanism of one of Nature's best catalysts  ...  relationships at key positions of the enzyme remote from the active site are an important first step towards testing the role of conformational change in OMPDC catalysis. 5.2  ... 
doi:10.1126/science.7809611 pmid:7809611 fatcat:ncclcwla7zdethlor7a3b44coy

Radical S-Adenosylmethionine Enzymes

Joan B. Broderick, Benjamin R. Duffus, Kaitlin S. Duschene, Eric M. Shepard
2014 Chemical Reviews  
This suggests that the Dph2-catalyzed reaction utilizing a [4Fe−4S] cluster and SAM is a case of convergent evolution, with Dph2 carrying out a similar type of catalytic mechanism but doing so in a manner  ...  (C) Spin quantitation of the EPR spectra in (A) for the amount of the [4Fe−4S] + cluster (+) and EPR spectra in (B) for the amount of glycyl radical ( ■ ) as a function of illumination time.  ...  We are grateful to funding agencies NIH (2R01GM054608-14) and DOE (DE-FG02-10ER16194) for support of our work on radical SAM enzymes. ABBREVIATIONS  ... 
doi:10.1021/cr4004709 pmid:24476342 pmcid:PMC4002137 fatcat:6tj52wfiyvegxfwjud2zzlx6mi

Glutathione catalysis and the reaction mechanisms of glutathione-dependent enzymes

Marcel Deponte
2013 Biochimica et Biophysica Acta - General Subjects  
Furthermore, several of the presented mechanisms could have implications for drug development. This article is part of a Special Issue entitled Cellular functions of glutathione.  ...  Ancient as well as recent structural changes of this fold did not only significantly alter the reaction mechanism, but also resulted in completely different protein functions.  ...  Acknowledgements I thank Tobias Dick, Heiner Schirmer, Luise Krauth-Siegel and the numerous other external and internal participants of the Heidelberg "Redox Biology Seminar" for their instructive presentations  ... 
doi:10.1016/j.bbagen.2012.09.018 pmid:23036594 fatcat:syhpjqbakze3dbmm3xrwxa4yry

The XTH Gene Family: An Update on Enzyme Structure, Function, and Phylogeny in Xyloglucan Remodeling

J. M. Eklof, H. Brumer
2010 Plant Physiology  
In the coming years, we look forward to the continued convergence of biochemical, protein structural, and physiological studies of these curious enzymes.  ...  A FUTURE FOR OLD-FASHIONED ENZYMOLOGY IN THESE MODERN TIMES OF FUNCTIONAL GENOMICS?  ... 
doi:10.1104/pp.110.156844 pmid:20421457 pmcid:PMC2879796 fatcat:3tftxxiwo5c2vht2lzsmfmidpi

Origins of Specificity and Promiscuity in Metabolic Networks

Pablo Carbonell, Guillaume Lecointre, Jean-Loup Faulon
2011 Journal of Biological Chemistry  
Significance: Learning about the mechanisms of enzyme evolution might assist us with the identification of primeval catalytic functions and minimal metabolism.  ...  To investigate this mechanism, we have explored the chemical diversity present in a largely unbiased data set of catalytic reactions processed by modern enzymes across the tree of life.  ...  Catalytic Function Classification and Efficiency Estimation-We used two types of functional classification for enzymes, one based on pathway modules and another on ortholog groups.  ... 
doi:10.1074/jbc.m111.274050 pmid:22052908 pmcid:PMC3243566 fatcat:c3sew5kimjarfkgfyqwmqsxxfu

Homology, Pathway Distance and Chromosomal Localization of the Small Molecule Metabolism Enzymes in Escherichia coli

Stuart C.G. Rison, Sarah A. Teichmann, Janet M. Thornton
2002 Journal of Molecular Biology  
In addition to transcriptional units, isozymes and inline reuse of enzymes provide mechanisms for controlling the SMM network.  ...  a different reaction in each instance), nine had multiple substrate specificity (i.e. catalysed the same reaction on different substrates in each instance) and one catalysed the same reaction on the same  ...  easily parseable E. coli transcriptional unit data to us; and Gail Bartlett and Annabel Todd for many useful enzyme-related discussions.  ... 
doi:10.1016/s0022-2836(02)00140-7 pmid:12054833 fatcat:qozcaqz4izevfb2xpvgp3sh4pm

The prokaryotic Mo/W-bisPGD enzymes family: A catalytic workhorse in bioenergetic

Stéphane Grimaldi, Barbara Schoepp-Cothenet, Pierre Ceccaldi, Bruno Guigliarelli, Axel Magalon
2013 Biochimica et Biophysica Acta - Bioenergetics  
Reaction mechanism proposed for FdhF with the activation step based on sulfur-shift process. Adapted from [102].  ...  This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones  ...  Acknowledgements We thank Wolfgang Nitschke, Bénédicte Burlat and Frédéric Biaso for helpful discussions.  ... 
doi:10.1016/j.bbabio.2013.01.011 pmid:23376630 fatcat:uf6fcwebjngv7obnpc277hn3eq

Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer

Anna Pabis, Fernanda Duarte, Shina C. L. Kamerlin
2016 Biochemistry  
Understanding the factors that underlie such multifunctionality is crucial both for understanding functional evolution in enzyme superfamilies and for the development of artificial enzymes.  ...  In this Current Topic, we have primarily focused on the structural and mechanistic basis for catalytic promiscuity among enzymes that facilitate both phosphoryl and sulfuryl transfer in the same active  ...  The overall reaction mechanisms for the hydrolysis of both phosphate and sulfate esters involve in-line nucleophilic displacement reactions, with differences of only a single atom or functional group between  ... 
doi:10.1021/acs.biochem.6b00297 pmid:27187273 pmcid:PMC4899807 fatcat:odxkx4rrhbfdxhsak3g75ai3si

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

C. Brasen, D. Esser, B. Rauch, B. Siebers
2014 Microbiology and Molecular Biology Reviews  
ACKNOWLEDGMENTS We are most grateful to all colleagues and friends who contributed to the understanding of archaeal metabolism and share enthusiasm for this fascinating domain of life.  ...  Esser was supported by the DFG (grant SI 642/10-1) and B. Rauch by the DFG GRK 1431 (Transcription, chromatin structure, and DNA repair in development and differentiation [UDE]).  ...  The catalytic mechanism of the ROK kinases seems to be similar to that described for ATP-GLK and HK (65) .  ... 
doi:10.1128/mmbr.00041-13 pmid:24600042 pmcid:PMC3957730 fatcat:6xfccw26jvczbgjm7hkbpr72ly

Modeling and Optimization of Directed Evolution Protocols [chapter]

Gregory Moore, Costas Maranas
2003 Enzyme Functionality  
in the N th PCR cycle or one that was already in the reaction mixture before the N th PCR cycle began. 61 2.4 The GC content of a DNA strand can significantly alter the number of mutations produced by  ...  total number of crossovers as a function of the number of silent mutations permitted.  ...  . & Monticello, D.J. (2001), "DNA shuffling method for generating highly recombined genes and evolved enzymes," Nat Biotechnol 19(4): 354-359.  ... 
doi:10.1201/9780203913048.ch8 fatcat:cmjrrnvkt5gxxhekgcntj6egyy

Prediction of protein function from protein sequence and structure

James C. Whisstock, Arthur M. Lesk
2003 Quarterly Reviews of Biophysics (print)  
Alternative methods include inferring conservation patterns in members of a functionally uncharacterized family for which many sequences and structures are known.  ...  In this article we review the state of the art in function prediction and describe some of the underlying difficulties and successes.  ...  The similarity of function and mechanism has arisen by convergent evolution.  ... 
doi:10.1017/s0033583503003901 pmid:15029827 fatcat:e3x65am2tvbkdfhcv6d5v5i3je
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