Connectivity between Catalytic Landscapes of the Metallo-β-Lactamase Superfamily

Baier, Florian; Tokuriki, Nobuhiko

doi:10.1016/j.jmb.2014.04.013

Cited by 102 publications

(176 citation statements)

References 63 publications

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“…We have learned that evolution is economical: related enzymes that catalyze different reactions share conserved functional elements, including catalytic or metal-binding residues, cofactors, and key residues that modulate the chemistry (Bartlett et al 2003). And today's members of functionally diverse families exhibit the catalytic promiscuity, often as a result of their mechanisms, conformational diversity, etc., that presumably fueled their divergence in the past (Babtie et al 2010;Baier & Tokuriki, 2014;Gatti-Lafranconi & Hollfelder, 2013;Tokuriki & Tawfik, 2009). Experiments lend credence to the proposal that promiscuity underlies much of enzyme innovation.…”

Section: Nature's Approach To Chemical Innovationmentioning

confidence: 68%

The nature of chemical innovation: new enzymes by evolution

Arnold

2015

Quart. Rev. Biophys.

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Abstract. I describe how we direct the evolution of non-natural enzyme activities, using chemical intuition and information on structure and mechanism to guide us to the most promising reaction/enzyme systems. With synthetic reagents to generate new reactive intermediates and just a few amino acid substitutions to tune the active site, a cytochrome P450 can catalyze a variety of carbene and nitrene transfer reactions. The cyclopropanation, N-H insertion, C-H amination, sulfimidation, and aziridination reactions now demonstrated are all well known in chemical catalysis but have no counterparts in nature. The new enzymes are fully genetically encoded, assemble and function inside of cells, and can be optimized for different substrates, activities, and selectivities. We are learning how to use nature's innovation mechanisms to marry some of the synthetic chemists' favorite transformations with the exquisite selectivity and tunability of enzymes.

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Section: Nature's Approach To Chemical Innovationmentioning

confidence: 68%

The nature of chemical innovation: new enzymes by evolution

Arnold

2015

Quart. Rev. Biophys.

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“…Based on screening of a set of representative enzymes (124 out of 900) against 17 putative substrates this study found that the family generally catalyzes the condensation of a β-keto acid with acetyl-CoA producing acetoacetate and CoA ester. Widespread catalytic promiscuity was described in the metallo-β-lactamase superfamily through the analyses of 24 enzymes against 10 catalytically distinct hydrolytic reactions where enzymes catalyzed on average 1.5 reactions in addition to their native activity (38). In an orthogonal study, screening of all 23 soluble HADSF members within a single species (E. coli) was performed with a set of 80 commercially available phosphorylated substrates (4).…”

Section: Discussionmentioning

confidence: 99%

Panoramic view of a superfamily of phosphatases through substrate profiling

Huang

Pandya

Liu

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

136

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Large-scale activity profiling of enzyme superfamilies provides information about cellular functions as well as the intrinsic binding capabilities of conserved folds. Herein, the functional space of the ubiquitous haloalkanoate dehalogenase superfamily (HADSF) was revealed by screening a customized substrate library against >200 enzymes from representative prokaryotic species, enabling inferred annotation of ∼35% of the HADSF. An extremely high level of substrate ambiguity was revealed, with the majority of HADSF enzymes using more than five substrates. Substrate profiling allowed assignment of function to previously unannotated enzymes with known structure, uncovered potential new pathways, and identified isofunctional orthologs from evolutionarily distant taxonomic groups. Intriguingly, the HADSF subfamily having the least structural elaboration of the Rossmann fold catalytic domain was the most specific, consistent with the concept that domain insertions drive the evolution of new functions and that the broad specificity observed in HADSF may be a relic of this process.evolution | specificity | phosphatase | substrate screen | promiscuity S ince the first genomes were sequenced, there has been an exponential increase in the number of protein sequences deposited into databases worldwide. At the time of this writing the UniProtKB/TrEMBL database contains over 32 million protein sequences. Although this increase in sequence data has dramatically enhanced our understanding of the genomic organization of organisms, as the number of protein sequences grows, the proportion of firm functional assignments diminishes. Traditionally, methods of functional annotation involve comparing sequence identity between experimentally characterized proteins and newly sequenced ones, typically via BLAST (1). In cases where significant sequence similarity cannot be ascertained, proteins are annotated as "hypothetical" or "putative." Moreover, the decrease in sequence identity leads to an increased uncertainty in functional assignment, especially as the phylogenetic distance between organisms grows, limiting iso-functional ortholog discovery.As the number of newly sequenced genomes grows larger, more protein sequences are likely to be misannotated, oftentimes resulting in the propagation of incorrect functional annotation across newly identified sequences. To tackle the problem of unannotated or misannotated proteins, newer methods for computational assignment have been created with varying degrees of success (2). Although these methods outperform historical methods, continued improvement is necessary to ensure accurate annotation of function (2). A greater swath of functional space can be covered by screening substrates in a high-throughput manner on multiple enzymes from a family (3, 4). Family-wide substrate profiling offers a data-rich resource. The use of sparse screening of sequence space and a diversified library permits the determination of substrate specificity profiles to provide a familywide view of the range of substrates...

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“…[100] The promiscuous reactions that different MbLs catalyse generally have lower k cat , where it is hypothesised that promiscuous substrates may not be well positioned relative to the nucleophilic hydroxide for catalysis. [105] Flexibility in metal ion coordination in MbLs enables catalysis of diverse compounds, albeit at a reduced efficiency, but this promiscuity would improve survival of host organisms challenged with new xenobiotic substrates, and provide a starting point for improvement over generations.…”

Section: Active Site Changes and Activity Divergencementioning

confidence: 99%

“…The ability to repurpose existing catalytic infrastructure for new or improved functionality is an efficient strategy from an evolutionary standpoint, and it may explain the many overlapping catalytic activities observed in metalloenzyme superfamilies. [105] …”

Section: Active Site Changes and Activity Divergencementioning

confidence: 99%

The Evolution of New Catalytic Mechanisms for Xenobiotic Hydrolysis in Bacterial Metalloenzymes

et al. 2016

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An increasing number of bacterial metalloenzymes have been shown to catalyse the breakdown of xenobiotics in the environment, while others exhibit a variety of promiscuous xenobiotic-degrading activities. Several different evolutionary processes have allowed these enzymes to gain or enhance xenobiotic-degrading activity. In this review, we have surveyed the range of xenobiotic-degrading metalloenzymes, and discuss the molecular and catalytic basis for the development of new activities. We also highlight how our increased understanding of the natural evolution of xenobiotic-degrading metalloenzymes can be been applied to laboratory enzyme design.

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Connectivity between Catalytic Landscapes of the Metallo-β-Lactamase Superfamily

Cited by 102 publications

References 63 publications

The nature of chemical innovation: new enzymes by evolution

The nature of chemical innovation: new enzymes by evolution

Panoramic view of a superfamily of phosphatases through substrate profiling

The Evolution of New Catalytic Mechanisms for Xenobiotic Hydrolysis in Bacterial Metalloenzymes

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