Mechanism of IS200/IS605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection

Barábas, O.; Ronning, Donald R.; Guynet, Catherine; Hickman, A.B.; Ton‐Hoang, Bao; Chandler, Michaël; Dyda, Fred

doi:10.1016/j.cell.2007.12.029

Cited by 133 publications

(203 citation statements)

References 30 publications

(47 reference statements)

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“…NtC AB1S, BBS1, BB2S and NS1S occur in guanine tetraplexes, while BB1S and BB2S are observed only in their G-G steps. BBS1 not only forms the G-quartet core of quadruplexes (PDB entry 1jpq; Haider et al, 2002), but it also accommodates a purine-purine mismatch (PDB entry 178d; McAuley-Hecht et al, 1994) and occurs in the loops of complicated self-folding single-stranded hairpin structures (PDB entry 2vju; Barabas et al, 2008).…”

Section: B-a: Conformers Bridging B-form To A-formmentioning

confidence: 99%

A DNA structural alphabet provides new insight into DNA flexibility

Schneider

Božíková

Nečasová

et al. 2018

Acta Cryst Sect D Struct Biol

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DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. To identify the DNA structural polymorphisms that are possible in such adaptations, the dinucleotide structures of 60 000 DNA steps from sequentially nonredundant crystal structures were classified and an automated protocol assigning 44 distinct structural (conformational) classes called NtC (for Nucleotide Conformers) was developed. To further facilitate understanding of the DNA structure, the NtC were assembled into the DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and the projection of CANA onto the graphical representation of the molecular structure was proposed. The NtC classification was used to define a validation score called confal, which quantifies the conformity between an analyzed structure and the geometries of NtC. NtC and CANA assignment were applied to analyze the structural properties of typical DNA structures such as Dickerson-Drew dodecamers, guanine quadruplexes and structural models based on fibre diffraction. NtC, CANA and confal assignment, which is accessible at the website https://dnatco.org, allows the quantitative assessment and validation of DNA structures and their subsequent analysis by means of pseudo-sequence alignment. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:2.

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Section: B-a: Conformers Bridging B-form To A-formmentioning

confidence: 99%

A DNA structural alphabet provides new insight into DNA flexibility

Schneider

Božíková

Nečasová

et al. 2018

Acta Cryst Sect D Struct Biol

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“…Similar to dUTPases, only a single metal ion is involved in the catalytic reaction of several enzymes, such as nucleases with the ββα-Me structural motifs, [71][72] or HUH motifs (where H's denote two histidine residues separated by a hydrophobic residue, U). 69,[73][74] An analogous role of the single metal ion in one-metal ion catalysis has been proposed to metal ion B in two-metal ion catalysis based on structural data. 8 An additional emerging role for metal ion B is to take on a more symmetrical coordination near the transition state region, and thereby to facilitate catalysis.…”

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confidence: 99%

Mutations Decouple Proton Transfer from Phosphate Cleavage in the dUTPase Catalytic Reaction

et al. 2015

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Most enzymes present a catalytic mechanism where one or more proton transfer events occur coupled tightly together with the enzymatic chemical reaction. We show here that inactivating mutations decouple this proton transfer step from the phosphate cleavage reaction in dUTPase. Homotrimeric dUTPase enzymes catalyze the hydrolysis of dUTP to dUMP and pyrophosphate, using largely similar structural and functional groups as most AAA+ enzymes. dUTPases typically use a single Mg 2+ ion as a cofactor in the active site that is formed by direct protein-protein contacts including all three protomers. Here we focus on the C-terminal arm structural motif, which has sequence and functional similarities to P-loop motifs, and is required for catalysis. In this work, we have studied the functional roles of the C-terminal arm in ligand binding and catalysis by using QM/MM (quantum mechanics/molecular mechanics) calculations in conjunction with site-directed mutagenesis experiments. We also present a new method to assess the metal ion coordination symmetry during the catalytic reaction. Using this new implementation, we identified that the coordination symmetry follows a consistent pattern in the three systems studied, reaching the most symmetrical state near the transition states. We found that the phosphate cleavage proceeds with a concerted bimolecular (A N D N ) mechanism with a loose dissociative transition state, and that it is coupled with a proton transfer step involving a unanimously conserved Asp residue. We show that the main mechanistic effect of the lack of the C-terminal arm is to decouple the phosphate cleavage from the subsequent proton transfer step, resulting in a highbarrier altered reaction pathway.

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“…1A), it is likely that their conformation will change significantly upon dimerization and they will acquire stable ordered conformation similar to those seen in Nuc. Such dimerization-induced ordering and assembly of active site residues would provide a clever regulatory mechanism that is also used by other nucleases (Barabas et al 2008;Rice and Correll 2008;Smits et al 2009) to prevent futile processing of cellular nucleic acids.…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of the primary piRNA biogenesis factor Zucchini reveals similarity to the bacterial PLD endonuclease Nuc

Voigt

Reuter

Kasaruho

et al. 2012

RNA

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Piwi-interacting RNAs (piRNAs) are a gonad-specific class of small RNAs that associate with the Piwi clade of Argonaute proteins and play a key role in transposon silencing in animals. Since biogenesis of piRNAs is independent of the doublestranded RNA-processing enzyme Dicer, an alternative nuclease that can process single-stranded RNA transcripts has been long sought. A Phospholipase D-like protein, Zucchini, that is essential for piRNA processing has been proposed to be a nuclease acting in piRNA biogenesis. Here we describe the crystal structure of Zucchini from Drosophila melanogaster and show that it is very similar to the bacterial endonuclease, Nuc. The structure also reveals that homodimerization induces major conformational changes assembling the active site. The active site is situated on the dimer interface at the bottom of a narrow groove that can likely accommodate single-stranded nucleic acid substrates. Furthermore, biophysical analysis identifies protein segments essential for dimerization and provides insights into regulation of Zucchini's activity.

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Mechanism of IS200/IS605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection

Cited by 133 publications

References 30 publications

A DNA structural alphabet provides new insight into DNA flexibility

A DNA structural alphabet provides new insight into DNA flexibility

Mutations Decouple Proton Transfer from Phosphate Cleavage in the dUTPase Catalytic Reaction

Crystal structure of the primary piRNA biogenesis factor Zucchini reveals similarity to the bacterial PLD endonuclease Nuc

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