4abt | pdb_00004abt

Crystal structure of Type IIF restriction endonuclease NgoMIV with cognate uncleaved DNA

spinqualitylabelsall models 4abt, resolution 2.22Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4abt is a 4 chain structure with sequence from "diplococcus_gonorrhoeae"_(zopf_1885)_lehmann_and_neumann_1896 "diplococcus gonorrhoeae" (zopf 1885) lehmann and neumann 1896. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CA Related: 1fiu Activity: Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [T2M4_NEIGO] Recognizes the double-stranded sequence GCCGGC and cleaves after G-1. Publication Abstract from PubMed 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. Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease.,Manakova E, Grazulis S, Zaremba M, Tamulaitiene G, Golovenko D, Siksnys V Nucleic Acids Res. 2012 Apr 11. PMID:22495930 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Endonuclease 3D structures

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