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The Evolution of Enzyme Function in the Isomerases

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The Evolution of Enzyme Function in the Isomerases Available online at www.sciencedirect.com ScienceDirect The evolution of enzyme function in the isomerases 1 2 Sergio Martinez Cuesta , Nicholas Furnham , 1 3 1 Syed Asad Rahman , Ian Sillitoe and Janet M Thornton The advent of computational approaches to measure functional chemical reaction is often changed by recruiting different similarity between enzymes adds a new dimension to existing catalytic residues within an active site, whilst conserving a evolutionary studies based on sequence and structure. This few residues required for the catalysis of at least one paper reviews research efforts aiming to understand the mechanistic step of the overall reaction [5]. Similarly, evolution of enzyme function in superfamilies, presenting a binding different substrates is commonly achieved by novel strategy to provide an overview of the evolution of changing the residues involved in substrate binding enzymes belonging to an individual EC class, using the and conserving residues involved in the overall reaction isomerases as an exemplar. [6]. There is substantial evidence supporting changes of Addresses the overall chemical reaction [7], as well as results report- 1 European Molecular Biology Laboratory, European Bioinformatics ing the importance of binding different substrates in the Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, evolution of function in superfamilies [8 ,9 ,10 ]. Com- Cambridge, CB10 1SD, United Kingdom 2 monly, enzyme superfamilies evolve by a combination of Department of Pathogen Molecular Biology, London School of Hygiene these two strategies [11,12]. For instance, phosphate & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom binding sites are often conserved, whilst the rest of the 3 Institute of Structural and Molecular Biology, Division of Biosciences, substrate can be changed during evolution [13,14]. University College London, Gower Street, London, WC1E 6BT, United Kingdom Other comprehensive studies on the variation of enzyme Corresponding authors: Martinez Cuesta, Sergio ([email protected]) sequence and structure [15,16 ] and plasticity of active and Thornton, ()Thornton, Janet M ([email protected]) sites [17,18 ] have also been fundamental in understand- ing how homologous enzymes accommodate alternative chemistries. Similarly, research on the convergent evolu- Current Opinion in Structural Biology 2014, 26:121–130 tion of enzyme mechanisms [19] and active sites [20] This review comes from a themed issue on Sequences and topology presented nature’s strategies to evolve different structural Edited by L Aravind and Christine A Orengo solutions for the catalysis of similar reactions [21,22 ,23]. For a complete overview see the Issue and the Editorial The widespread interest in understanding the evolution and chemistry of enzymes has led to large scale colla- Available online 5th July 2014 borative projects such as the Enzyme Function Initiative http://dx.doi.org/10.1016/j.sbi.2014.06.002 (EFI) [24] which aims to determine enzyme function 0959-440X/# 2014 The Authors. Published by Elsevier Ltd. This is an using both experimental and computational approaches. open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/). Starting from a comprehensive alignment of genomic regions, Zhao and co-workers from the EFI have ident- ified the epimerase activity, pathway context and bio- logical role in osmoprotection of a structurally Introduction characterised enzyme of unknown function from P. ber- Enzymes are life’s workforce. They catalyse the bio- mudensis using a combination of virtual screening, meta- chemical reactions that are the basis of metabolism in all bolomics, transcriptomics and biochemical experiments living organisms. The major route for creating new enzyme [25]. functions is gene duplication and subsequent evolution of one enzyme to another with a novel, though usually related, To explore this area further, we review our current knowl- function. Under the pressures of survival and reproduction, edge of the evolution of the isomerase class of reactions, innovating new functions at the metabolic level allows using newly developed computational tools to compare organisms to adapt to an environment of changing chemical enzyme reactions [26 ] and their evolution [27]. This is a conditions [1]; for example, bacterial resistance to man- specialised class of enzymes, which catalyse geometrical made chemicals such as drugs or pesticides. and structural rearrangements between isomers. Previous work Biological relevance of isomerases Previous studies focusing on analysing enzyme super- Isomerases are present in the metabolism and genome of families [2,3] and directed evolution experiments [4] most living organisms, catalysing up to 4% of the bio- discovered aspects of how enzyme evolution is influenced chemical reactions present in central metabolism, in by aspects of the chemistry of enzymes. The overall particular, carbohydrate metabolism. They also play a www.sciencedirect.com Current Opinion in Structural Biology 2014, 26:121–130 122 Sequences and topology Figure 1 (a) (b) H. sapiens E. coli 9% 4.9% 13.2% 2.6% 6.2% 20.2% 3.2% 9.3% 34.7% 37.4% 26.3% 33% Oxidoreductases (EC 1.b.c.d) Tranferases (EC 2.b.c.d) Hydrolases (EC 3.b.c.d) Lyases (EC 4.b.c.d) Isomerases (EC 5.b.c.d) Isomerases (4% of all enzymes in central metabolism) Ligases (EC 6.b.c.d) (c) (d) 5.1.1 Acting on amino acids and derivatives 5.1.2 Alanine racemase (EC 5.1.1.1) 5.1 Acting on hydroxy acids and derivatives Racemases and 5.1.3 O O epimerases Acting on carbohydrates and derivatives 5.1.99 CH3 CH3 Acting on other compounds HO(S) HO (R) 5.2 5.2.1 Cis-trans Cis-trans isomerases NH2 NH2 isomerases 5.3.1 L-alanine D-alanine Interconverting aldoses and ketoses 5.3.2 Interconverting keto- and enol-groups 5.3 5.3.3 Intramolecular Transposing C=C bonds oxidoreductases 5.3.4 Transposing S-S bonds Bond changes 5 5.3.99 Reaction centres Isomerases C(R/S) Other intramolecular oxidoreductases C C 5.4.1 Transferring acyl groups Structure 5.4.2 Phosphotransferases (phosphomutases) substrates and products N N 5.4 5.4.3 O H O H Intramolecular Transferring amino groups O O H H transferases 5.4.4 H H Transferring hydroxy groups O O 5.4.99 O O H H H H Transferring other groups N N N N 5.5 5.5.1 H H H H Intramolecular lyases Intramolecular lyases 5.99 5.99.1 Other isomerases Sole sub-subclass Current Opinion in Structural Biology Biological importance of isomerases. (a) Core metabolic pathways (the isomerase reactions are emboldened in black). Carbohydrate and terpenoid/ polyketide metabolic pathways are highlighted in blue and green squares, (b) Distribution of known enzymes in the human and E. coli genomes, (c) EC classification of isomerases. (d) Bond changes, reaction centres and structure of substrates and products obtained from the reaction catalysed by alanine racemase (EC 5.1.1.1) using EC-BLAST. crucial role in the metabolism of terpenoids and polyke- genes correspond to enzymes, this value increases to tides that are important in generating secondary metab- 37% in bacteria (Figure 1b). olites, especially in plants (Figure 1a). The Nomenclature Committee of the International The relative proportion of enzymes encoding for isomer- Union of Biochemistry and Molecular Biology (NC- ase activity depends on the species. Whereas 2.6% of the IUBMB) maintains the most widely used functional genes encoding for enzymatic activity corresponds to classification of isomerases in the Enzyme Commission isomerases in Homo sapiens, this proportion is higher in (EC) classification system [28]. Isomerases belong to the bacterial genomes such as Escherichia coli where they EC 5 primary class and they are grouped according to the account for 6.2%. These figures correlate with the relative chemistry of the reactions that they catalyse. They are proportion of protein-coding genes encoding for enzy- subdivided in three hierarchical levels: 6 subclasses, 17 matic activity in general. Whereas in human, 20% of sub-subclasses and 231 serial numbers (Figure 1c). These Current Opinion in Structural Biology 2014, 26:121–130 www.sciencedirect.com The evolution of enzyme function in the isomerases Martinez Cuesta et al. 123 serial numbers are associated with almost 300 bio- haloacid dehalogenase, crotonase, vicinal oxygen chelate, chemical reactions — for example EC 5.1.1.9 describes amidohydrolase, alkaline phosphatase, cupin, short-chain the racemisation of arginine, lysine or ornithine and it is dehydrogenase/reductase and PLP-dependent aspartate therefore linked to three distinct reactions. amino-transferase superfamilies [23,40,41,42 ,43]. From a practical viewpoint, the total number of isomerase Methods for analysing sequence, structure EC numbers (231) is small compared to other EC classes, and functional relationships which makes them attractive for manual analysis. Three Protein similarity networks have been used very success- of the six isomerase EC subclasses are similar to three EC fully to map biological information to large sets of proteins primary classes (intramolecular oxidoreductases — EC [44,43]. However, it is also necessary to include associated 5.3 are designated from oxidoreductases — EC 1; intra- changes of catalytic function during evolution preferably molecular transferases — EC 5.4 from transferases — EC in an automated fashion. FunTree is a resource devel- 2; and intramolecular lyases — EC 5.5 from lyases — EC oped to accomplish that goal [27] and it is maintained in 4, but refer to intramolecular
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