Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme
TLDR
The structure rationalizes the different specificities of T4 and eukaryotic Pnk and suggests a model for the assembly of the tetramer.Abstract:
T4 polynucleotide kinase (Pnk), in addition to being an invaluable research tool, exemplifies a family of bifunctional enzymes with 5′-kinase and 3′-phosphatase activities that play key roles in RNA and DNA repair. T4 Pnk is a homotetramer composed of a C-terminal phosphatase domain and an N-terminal kinase domain. The 2.0 Å crystal structure of the isolated kinase domain highlights a tunnel-like active site through the heart of the enzyme, with an entrance on the 5′ OH acceptor side that can accommodate a single-stranded polynucleotide. The active site is composed of essential side chains that coordinate the β phosphate of the NTP donor and the 3′ phosphate of the 5′ OH acceptor, plus a putative general acid that activates the 5′ OH. The structure rationalizes the different specificities of T4 and eukaryotic Pnk and suggests a model for the assembly of the tetramer.read more
Citations
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Evolution and classification of P-loop kinases and related proteins.
TL;DR: It is shown that kinases and some related proteins comprise a monophyletic assemblage within the P-loop NTPase fold, and an evolutionary classification of these proteins was developed using standard phylogenetic methods, analysis of shared sequence and structural signatures, and similarity-based clustering resulted in the identification of approximately 40 distinct protein families within theP-loop kinase class.
Journal ArticleDOI
The Molecular Architecture of the Mammalian DNA Repair Enzyme, Polynucleotide Kinase
N. K. Bernstein,R. Scott Williams,Melissa L. Rakovszky,Diana Cui,R. Green,Feridoun Karimi-Busheri,Rajam S. Mani,Sarah Galicia,C. Anne Koch,Carol E. Cass,Daniel Durocher,Michael Weinfeld,J. N. Mark Glover +12 more
TL;DR: The crystal structure of intact mammalian PNK and the structure of the PNK FHA bound to a cognate phosphopeptide are described and it is shown that the FHA domain exhibits a mode of target selection based on electrostatic complementarity between the binding surface and the phosphothreonine peptide.
Journal ArticleDOI
Tidying up loose ends: the role of polynucleotide kinase/phosphatase in DNA strand break repair
TL;DR: Polynucleotide kinase/phosphatase (PNKP) serves a crucial role in the repair of DNA strand breaks by catalyzing the restoration of 5'-phosphate and 3'-hydroxyl termini.
Journal ArticleDOI
Sensitive and rapid screening of T4 polynucleotide kinase activity and inhibition based on coupled exonuclease reaction and graphene oxide platform.
TL;DR: The as-proposed platform provides a universal platform for monitoring activity and inhibition of nucleotide kinase but also shows great potential in biological process researches, drug discovery, and clinic diagnostics.
Journal ArticleDOI
3'-Processing and strand transfer catalysed by retroviral integrase in crystallo.
TL;DR: A crystal structure of prototype foamy virus IN bound to viral DNA prior to 3′‐processing is reported and a striking substrate mimicry utilized by the inhibitors in their binding to the IN active site is highlighted.
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