3nic Citations

Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI.

Structure 18 1321-31 (2010)
Related entries: 3mx1, 3mx4

Cited: 32 times
EuropePMC logo PMID: 20800503

Abstract

The GIY-YIG endonuclease family comprises hundreds of diverse proteins and a multitude of functions; none have been visualized bound to DNA. The structure of the GIY-YIG restriction endonuclease R.Eco29kI has been solved both alone and bound to its target site. The protein displays a domain-swapped homodimeric structure with several extended surface loops encircling the DNA. Only three side chains from each protein subunit contact DNA bases, two directly and one via a bridging solvent molecule. Both tyrosine residues within the GIY-YIG motif are positioned in the catalytic center near a putative nucleophilic water; the remainder of the active site resembles the HNH endonuclease family. The structure illustrates how the GIY-YIG scaffold has been adapted for the highly specific recognition of a DNA restriction site, in contrast to nonspecific DNA cleavage by GIY-YIG domains in homing endonucleases or structure-specific cleavage by DNA repair enzymes such as UvrC.

Articles - 3nic mentioned but not cited (6)

  1. Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI. Mak AN, Lambert AR, Stoddard BL. Structure 18 1321-1331 (2010)
  2. Structural and Mechanistic Analysis of the Slx1-Slx4 Endonuclease. Gaur V, Wyatt HDM, Komorowska W, Szczepanowski RH, de Sanctis D, Gorecka KM, West SC, Nowotny M. Cell Rep 10 1467-1476 (2015)
  3. Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease. Gaur V, Ziajko W, Nirwal S, Szlachcic A, Gapińska M, Nowotny M. Nucleic Acids Res 47 11681-11690 (2019)
  4. Divalent metal ion differentially regulates the sequential nicking reactions of the GIY-YIG homing endonuclease I-BmoI. Kleinstiver BP, Bérubé-Janzen W, Fernandes AD, Edgell DR. PLoS One 6 e23804 (2011)
  5. Holliday junction resolution by At-HIGLE: an SLX1 lineage endonuclease from Arabidopsis thaliana with a novel in-built regulatory mechanism. Verma P, Kumari P, Negi S, Yadav G, Gaur V. Nucleic Acids Res 50 4630-4646 (2022)
  6. Structural and functional insights into the activation of the dual incision activity of UvrC, a key player in bacterial NER. Seck A, De Bonis S, Stelter M, Ökvist M, Senarisoy M, Hayek MR, Le Roy A, Martin L, Saint-Pierre C, Silveira CM, Gasparutto D, Todorovic S, Ravanat JL, Timmins J. Nucleic Acids Res 51 2931-2949 (2023)


Reviews citing this publication (6)

  1. Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification. Stoddard BL. Structure 19 7-15 (2011)
  2. Type II restriction endonucleases--a historical perspective and more. Pingoud A, Wilson GG, Wende W. Nucleic Acids Res 42 7489-7527 (2014)
  3. Homing endonucleases: from genetic anomalies to programmable genomic clippers. Belfort M, Bonocora RP. Methods Mol Biol 1123 1-26 (2014)
  4. Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms. Taylor GK, Stoddard BL. Nucleic Acids Res 40 5189-5200 (2012)
  5. Holliday junction-resolving enzymes-structures and mechanisms. Lilley DMJ. FEBS Lett 591 1073-1082 (2017)
  6. Structure and mechanism of nucleases regulated by SLX4. Nowotny M, Gaur V. Curr Opin Struct Biol 36 97-105 (2016)

Articles citing this publication (20)



Related citations provided by authors (1)