The evolution of enzyme function in the isomerases

被引：29

作者：

Cuesta, Sergio Martinez ^{[1
]}

Furnham, Nicholas ^{[2
]}

Rahman, Syed Asad ^{[1
]}

Sillitoe, Ian ^{[3
]}

Thornton, Janet M. ^{[1
]}

机构：

[1] European Bioinformat Inst EMB LEBI, European Mol Biol Lab, Cambridge CB10 1SD, England

[2] London Sch Hyg & Trop Med, Dept Pathogen Mol Biol, London WC1E 7HT, England

[3] UCL, Div Biosci, Inst Struct & Mol Biol, London WC1E 6BT, England

来源：

CURRENT OPINION IN STRUCTURAL BIOLOGY | 2014年 / 26卷

基金：

英国惠康基金;

关键词：

DIVERGENT EVOLUTION; CATALYTIC PROMISCUITY; CLASSIFICATION; DISCOVERY; SUPERFAMILIES; CONVERGENCE; PLASTICITY; CONVERSION; DIVERSITY; RACEMASE;

D O I：

10.1016/j.sbi.2014.06.002

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The advent of computational approaches to measure functional similarity between enzymes adds a new dimension to existing evolutionary studies based on sequence and structure. 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 individual EC class, using the isomerases as an exemplar.

引用

页码：121 / 130

页数：10

共 61 条

[1] Toward mechanistic classification of enzyme functions
Almonacid, Daniel E.
Babbitt, Patricia C.
[J]. CURRENT OPINION IN CHEMICAL BIOLOGY, 2011, 15 (03) : 435 - 442
[2] Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function
Almonacid, Daniel E.
Yera, Emmanuel R.
Mitchell, John B. O.
Babbitt, Patricia C.
[J]. PLOS COMPUTATIONAL BIOLOGY, 2010, 6 (03)
[3] Specificity in Transition State Binding: The Pauling Model Revisited
Amyes, Tina L.
Richard, John P.
[J]. BIOCHEMISTRY, 2013, 52 (12) : 2021 - 2035
[4] Update on activities at the Universal Protein Resource (UniProt) in 2013
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
[J]. NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) : D43 - D47
[5] Definitions of enzyme function for the structural genomics era
Babbitt, PC
[J]. CURRENT OPINION IN CHEMICAL BIOLOGY, 2003, 7 (02) : 230 - 237
[6] The ENZYME database in 2000
Bairoch, A
[J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 304 - 305
[7] Catalysing new reactions during evolution: Economy of residues and mechanism
Bartlett, GJ
Borkakoti, N
Thornton, JM
[J]. JOURNAL OF MOLECULAR BIOLOGY, 2003, 331 (04) : 829 - 860
[8] The generation of new protein functions by the combination of domains
Bashton, Matthew
Chothia, Cyrus
[J]. STRUCTURE, 2007, 15 (01) : 85 - 99
[9] Revealing the hidden functional diversity of an enzyme family
Bastard K.
Smith A.A.T.
Vergne-Vaxelaire C.
Perret A.
Zaparucha A.
De Melo-Minardi R.
Mariage A.
Boutard M.
Debard A.
Lechaplais C.
Pelle C.
Pellouin V.
Perchat N.
Petit J.-L.
Kreimeyer A.
Medigue C.
Weissenbach J.
Artiguenave F.
De Berardinis V.
Vallenet D.
Salanoubat M.
[J]. Nature Chemical Biology, 2014, 10 (1) : 42 - 49
[10] The Future of the Protein Data Bank
Berman, Helen M.
Kleywegt, Gerard J.
Nakamura, Haruki
Markley, John L.
[J]. BIOPOLYMERS, 2013, 99 (03) : 218 - 222

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