3V1Z: Crystal Structure Of Type Iif Restriction Endonuclease Bse634i With Cognate Dna

Restriction endonuclease Bse634I recognizes and cleaves the degenerate DNA sequence 5'-R/CCGGY-3' (R stands for A or G; Y for T or C, '/' indicates a cleavage position). Here, we report the crystal structures of the Bse634I R226A mutant complexed with cognate oligoduplexes containing ACCGGT and GCCGGC sites, respectively. In the crystal, all potential H-bond donor and acceptor atoms on the base edges of the conserved CCGG core are engaged in the interactions with Bse634I amino acid residues located on the alpha6 helix. In contrast, direct contacts between the protein and outer base pairs are limited to van der Waals contact between the purine nucleobase and Pro203 residue in the major groove and a single H-bond between the O2 atom of the outer pyrimidine and the side chain of the Asn73 residue in the minor groove. Structural data coupled with biochemical experiments suggest that both van der Waals interactions and indirect readout contribute to the discrimination of the degenerate base pair by Bse634I. Structure comparison between related enzymes Bse634I (R/CCGGY), NgoMIV (G/CCGGC) and SgrAI (CR/CCGGYG) reveals how different specificities are achieved within a conserved structural core.
PDB ID: 3V1ZDownload
MMDB ID: 99008
PDB Deposition Date: 2011/12/11
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 2.2  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 3V1Z: tetrameric; determined by author and by software (PISA)
Molecular Components in 3V1Z
Label Count Molecule
Proteins (2 molecules)
Endonuclease Bse634ir
Molecule annotation
Nucleotide(1 molecule)
DNA (5'-d(*tp*cp*gp*cp*gp*cp*cp*gp*gp*cp*gp*cp*g)-3')
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB