Characterising Complex Enzyme Reaction Data

被引：11

作者：

Donertas, Handan Melike ^{[1
,2
]}

Cuesta, Sergio Martinez ^{[1
,3
]}

Rahman, Syed Asad ^{[1
]}

Thornton, Janet M. ^{[1
]}

机构：

[1] European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge, England

[2] Middle E Tech Univ, Dept Biol Sci, TR-06531 Ankara, Turkey

[3] Univ Cambridge, Canc Res UK Cambridge Inst, Li Ka Shing Ctr, Cambridge, England

来源：

PLOS ONE | 2016年 / 11卷 / 02期

关键词：

GENOME-SCALE CLASSIFICATION; METABOLIC REACTIONS; CATALYTIC PROMISCUITY; EC NUMBERS; PREDICTION; EVOLUTION; TOOL; CHLOROPEROXIDASE; REPRESENTATION; PURIFICATION;

D O I：

10.1371/journal.pone.0147952

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The relationship between enzyme-catalysed reactions and the Enzyme Commission (EC) number, the widely accepted classification scheme used to characterise enzyme activity, is complex and with the rapid increase in our knowledge of the reactions catalysed by enzymes needs revisiting. We present a manual and computational analysis to investigate this complexity and found that almost one-third of all known EC numbers are linked to more than one reaction in the secondary reaction databases (e.g., KEGG). Although this complexity is often resolved by defining generic, alternative and partial reactions, we have also found individual EC numbers with more than one reaction catalysing different types of bond changes. This analysis adds a new dimension to our understanding of enzyme function and might be useful for the accurate annotation of the function of enzymes and to study the changes in enzyme function during evolution.

引用

页数：18

共 76 条

[1] Rhea-a manually curated resource of biochemical reactions [J].

Alcantara, Rafael ;

Axelsen, Kristian B. ;

Morgat, Anne ;

Belda, Eugeni ;

Coudert, Elisabeth ;

Bridge, Alan ;

Cao, Hong ;

de Matos, Paula ;

Ennis, Marcus ;

Turner, Steve ;

Owen, Gareth ;

Bougueleret, Lydie ;

Xenarios, Ioannis ;

Steinbeck, Christoph .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D754-D760

[2] The COMBREX Project: Design, Methodology, and Initial Results [J].

Anton, Brian P. ;

Chang, Yi-Chien ;

Brown, Peter ;

Choi, Han-Pil ;

Faller, Lina L. ;

Guleria, Jyotsna ;

Hu, Zhenjun ;

Klitgord, Niels ;

Levy-Moonshine, Ami ;

Maksad, Almaz ;

Mazumdar, Varun ;

McGettrick, Mark ;

Osmani, Lais ;

Pokrzywa, Revonda ;

Rachlin, John ;

Swaminathan, Rajeswari ;

Allen, Benjamin ;

Housman, Genevieve ;

Monahan, Caitlin ;

Rochussen, Krista ;

Tao, Kevin ;

Bhagwat, Ashok S. ;

Brenner, Steven E. ;

Columbus, Linda ;

de Crecy-Lagard, Valerie ;

Ferguson, Donald ;

Fomenkov, Alexey ;

Gadda, Giovanni ;

Morgan, Richard D. ;

Osterman, Andrei L. ;

Rodionov, Dmitry A. ;

Rodionova, Irina A. ;

Rudd, Kenneth E. ;

Soll, Dieter ;

Spain, James ;

Xu, Shuang-Yong ;

Bateman, Alex ;

Blumenthal, Robert M. ;

Bollinger, J. Martin ;

Chang, Woo-Suk ;

Ferrer, Manuel ;

Friedberg, Iddo ;

Galperin, Michael Y. ;

Gobeill, Julien ;

Haft, Daniel ;

Hunt, John ;

Karp, Peter ;

Klimke, William ;

Krebs, Carsten ;

Macelis, Dana .

PLOS BIOLOGY, 2013, 11 (08)

[3] Update on activities at the Universal Protein Resource (UniProt) in 2013 [J].

Apweiler, Rolf ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Alam-Faruque, Yasmin ;

Alpi, Emanuela ;

Antunes, Ricardo ;

Arganiska, Joanna ;

Casanova, Elisabet Barrera ;

Bely, Benoit ;

Bingley, Mark ;

Bonilla, Carlos ;

Britto, Ramona ;

Bursteinas, Borisas ;

Chan, Wei Mun ;

Chavali, Gayatri ;

Cibrian-Uhalte, Elena ;

Da Silva, Alan ;

De Giorgi, Maurizio ;

Dimmer, Emily ;

Fazzini, Francesco ;

Gane, Paul ;

Fedotov, Alexander ;

Castro, Leyla Garcia ;

Garmiri, Penelope ;

Hatton-Ellis, Emma ;

Hieta, Reija ;

Huntley, Rachael ;

Jacobsen, Julius ;

Jones, Rachel ;

Legge, Duncan ;

Liu, Wudong ;

Luo, Jie ;

MacDougall, Alistair ;

Mutowo, Prudence ;

Nightingale, Andrew ;

Orchard, Sandra ;

Patient, Samuel ;

Pichler, Klemens ;

Poggioli, Diego ;

Pundir, Sangya ;

Pureza, Luis ;

Qi, Guoying ;

Rosanoff, Steven ;

Sawford, Tony ;

Sehra, Harminder ;

Turner, Edward ;

Volynkin, Vladimir ;

Wardell, Tony ;

Watkins, Xavier .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D43-D47

[4] A large-scale protein-function database [J].

Apweiler, Rolf ;

Armstrong, Richard ;

Bairoch, Amos ;

Cornish-Bowden, Athel ;

Halling, Peter J. ;

Hofmeyr, Jan-Hendrik S. ;

Kettner, Carsten ;

Leyh, Thomas S. ;

Rohwer, Johann ;

Schomburg, Dietmar ;

Steinbeck, Christoph ;

Tipton, Keith .

NATURE CHEMICAL BIOLOGY, 2010, 6 (11) :785-785

[5] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[6] Definitions of enzyme function for the structural genomics era [J].

Babbitt, PC .

CURRENT OPINION IN CHEMICAL BIOLOGY, 2003, 7 (02) :230-237

[7] Revealing the hidden functional diversity of an enzyme family [J].

Bastard, Karine ;

Smith, Adam Alexander Thil ;

Vergne-Vaxelaire, Carine ;

Perret, Alain ;

Zaparucha, Anne ;

De Melo-Minardi, Raquel ;

Mariage, Aline ;

Boutard, Magali ;

Debard, Adrien ;

Lechaplais, Christophe ;

Pelle, Christine ;

Pellouin, Virginie ;

Perchat, Nadia ;

Petit, Jean-Louis ;

Kreimeyer, Annett ;

Medigue, Claudine ;

Weissenbach, Jean ;

Artiguenave, Franois ;

De Berardinis, Veronique ;

Vallenet, David ;

Salanoubat, Marcel .

NATURE CHEMICAL BIOLOGY, 2014, 10 (01) :42-U77

[8] Reconciliation of metabolites and biochemical reactions for metabolic networks [J].

Bernard, Thomas ;

Bridge, Alan ;

Morgat, Anne ;

Moretti, Sebastien ;

Xenarios, Ioannis ;

Pagni, Marco .

BRIEFINGS IN BIOINFORMATICS, 2014, 15 (01) :123-135

[9] Graphical representation standards for chemical structure diagrams [J].

Brecher, Jonathan .

PURE AND APPLIED CHEMISTRY, 2008, 80 (02) :277-410

[10] Automatic reaction mapping and reaction center detection [J].

Chen, William Lingran ;

Chen, David Z. ;

Taylor, Keith T. .

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2013, 3 (06) :560-593

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