3NIC

DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F

Summary for 3NIC

• Entry DOI: 10.2210/pdb3nic/pdb
• Related: 3MX1 3MX4
• Descriptor: Eco29kIR, DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3'), ... (5 entities in total)
• Functional Keywords: type ii restriction endonuclease, giy-yig endonuclease, dna-bound, hydrolase-dna complex, hydrolase/dna
• Biological source: Escherichia coli
• Total number of polymer chains: 16
• Total formula weight: 269451.14

Authors

Mak, A.N.S.,Lambert, A.R.,Stoddard, B.L. (deposition date: 2010-06-15, release date: 2010-09-08, Last modification date: 2024-04-03)

Primary citation

Mak, A.N.,Lambert, A.R.,Stoddard, B.L.
Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI.
Structure, 18:1321-1331, 2010

PubMed 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.

PubMed: 20800503
DOI: 10.1016/j.str.2010.07.006

Experimental method

X-RAY DIFFRACTION (2.8 Å)