Arginine as a General Acid Catalyst in Serine Recombinase-mediated DNA Cleavage

Keenholtz, Ross A.; Mouw, Kent W.; Boocock, Martin R.; Li, Nan‐Sheng; Piccirilli, Joseph A.; Rice, Phoebe A.

doi:10.1074/jbc.m113.508028

Cited by 30 publications

(33 citation statements)

References 43 publications

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“…Lee et al, 2013). Although not often found in this catalytic role, some precedent exists in other enzyme systems (Keenholtz et al, 2013; Silva, Schulz, Jahn, Jahn, & Ramos, 2010). In addition to its proximity to the site of phosphoryl transfer, this residue appears to be absolutely conserved across the PHM superfamily (Fig.…”

Section: Catalytic Mechanismmentioning

confidence: 99%

Biology, Mechanism, and Structure of Enzymes in the α- d -Phosphohexomutase Superfamily

Stiers

Muenks

Beamer

2017

Advances in Protein Chemistry and Structural Biology

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Enzymes in the α-D-phosphohexomutases (PHM) superfamily catalyze the reversible conversion of phosphosugars, such as glucose 1-phosphate and glucose 6-phosphate. These reactions are fundamental to primary metabolism across the kingdoms of life, and are required for a myriad of cellular processes, ranging from exopolysaccharide production to protein glycosylation. The subject of extensive mechanistic characterization during the latter half of the twentieth century, these enzymes have recently benefitted from biophysical characterization, including X-ray crystallography, NMR, and hydrogen-deuterium exchange studies. This work has provided new insights into the unique catalytic mechanism of the superfamily, shed light on the molecular determinants of ligand recognition, and revealed the evolutionary conservation of conformational flexibility. Novel associations with inherited metabolic disease and the pathogenesis of bacterial infections have emerged, spurring renewed interest in the long-appreciated functional roles of these enzymes.

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Section: Catalytic Mechanismmentioning

confidence: 99%

Biology, Mechanism, and Structure of Enzymes in the α- d -Phosphohexomutase Superfamily

Stiers

Muenks

Beamer

2017

Advances in Protein Chemistry and Structural Biology

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“…In the Sin active site, R7 is well-positioned to abstract a proton from the nucleophilic serine as it attacks, R66 to hold the scissile phosphate in place and stabilize the transition state, and R69 and R66 to donate a proton to the DNA 3′ oxygen as it leaves. Evidence that R69 is important in stabilizing the leaving group (during the cleavage reaction) and likely to be the general acid was supplied by experiments replacing the 3′O with an S, which is predicted to be a better leaving group in the absence of a general acid (76). Mutants of R69, but not of other arginines, were partially rescued by the 3′S (although it should be noted that R66 mutants were simply inactive with all substrates).…”

Section: Activation and Catalysismentioning

confidence: 99%

Serine Resolvases

Rice

2015

Microbiol Spectr

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Serine resolvases are an interesting group of site-specific recombinases that, in their native contexts, resolve large fused replicons into smaller separated ones. Some resolvases are encoded by replicative transposons and resolve the transposition product, in which the donor and recipient molecules are fused, into separate replicons. Other resolvases are encoded by plasmids and function to resolve plasmid dimers into monomers. Both types are therefore involved in the spread and maintenance of antibiotic-resistance genes. Resolvases and the closely related invertases were the first serine recombinases to be studied in detail, and much of our understanding of the unusual strand exchange mechanism of serine recombinases is owed to those early studies. Resolvases and invertases have also served as paradigms for understanding how DNA topology can be harnessed to regulate enzyme activity. Finally, their relatively modular structure, combined with a wealth of structural and biochemical data, has made them good choices for engineering chimeric recombinases with designer specificity. This chapter focuses on the current understanding of serine resolvases, with a focus on the contributions of structural studies.

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“…No divalent metal ion or any other cofactors are required, and key roles in catalysis are played by an array of arginine residues at the active site (56,57). The resolution of the covalent intermediate by a terminal 3′-OH group of another strand results in strand transfer.…”

Section: Serine Transposasesmentioning

confidence: 99%

Mechanisms of DNA Transposition

Hickman

Dyda

2015

Microbiol Spectr

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DNA transposases use a limited repertoire of structurally and mechanistically distinct nuclease domains to catalyze the DNA strand breaking and rejoining reactions that comprise DNA transposition. Here, we review the mechanisms of the four known types of transposition reactions catalyzed by (1) RNase H-like transposases (also known as DD(E/D) enzymes); (2) HUH single-stranded DNA transposases; (3) serine transposases; and (4) tyrosine transposases. The large body of accumulated biochemical and structural data, particularly for the RNase H-like transposases, has revealed not only the distinguishing features of each transposon family, but also some emerging themes that appear conserved across all families. The more-recently characterized single-stranded DNA transposases provide insight into how an ancient HUH domain fold has been adapted for transposition to accomplish excision and then site-specific integration. The serine and tyrosine transposases are structurally and mechanistically related to their cousins, the serine and tyrosine site-specific recombinases, but have to date been less intensively studied. These types of enzymes are particularly intriguing as in the context of site-specific recombination they require strict homology between recombining sites, yet for transposition can catalyze the joining of transposon ends to form an excised circle and then integration into a genomic site with much relaxed sequence specificity.In this chapter, we provide an overview of the fundamental concepts of DNA transposition mechanisms. Our aim is to emphasize basic themes and, in this effort, we will focus on specific illustrative cases rather than attempt an exhaustive review of the literature. We hope that the selected references will point the curious reader towards the landmark studies in the field as well as some of the most exciting recent results. We also direct the reader to other recent reviews (1-3).DNA transposases are enyzmes that move discrete segments of DNA called transposons from one location in the genome (often called the donor site) to a new site without using RNA intermediates. DNA transposases are usually encoded by the mobile element itself (in which case they are "autonomous" transposons). However, some transposons are missing a self-encoded transposase yet have ends that can be recognized by a transposase encoded somewhere else in the genome, and thus are "non-autonomous" (Siguier et al., this volume). Although logic suggests that all DNA transposons are moved by transposases, the term was originally reserved for those enzymes that do not require significant regions of homology between any part of the transposon and the sites to which they are moved, the so-called target (or insertion or integration) sites. As biology is not always neat and tidy, transposases can exhibit a spectrum of homology requirements and vagaries of terminology have arisen such that certain transposases are sometimes referred to as "resolvases" or by the generic term "recombinases".From a mechanistic perspective, t...

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Arginine as a General Acid Catalyst in Serine Recombinase-mediated DNA Cleavage

Cited by 30 publications

References 43 publications

Biology, Mechanism, and Structure of Enzymes in the α- d -Phosphohexomutase Superfamily

Biology, Mechanism, and Structure of Enzymes in the α- d -Phosphohexomutase Superfamily

Serine Resolvases

Mechanisms of DNA Transposition

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