2VLA

Crystal structure of restriction endonuclease BpuJI recognition domain in complex with cognate DNA

Summary for 2VLA

• Entry DOI: 10.2210/pdb2vla/pdb
• Descriptor: RESTRICTION ENDONUCLEASE R.BPUJI, 5'-D(*GP*GP*TP*AP*CP*CP*CP*GP*TP*GP *GP*A)-3', 5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*AP *CP*C)-3', ... (6 entities in total)
• Functional Keywords: restriction endonuclease, hydrolase, endonuclease, dna recognition, helix-turn-helix
• Biological source: BACILLUS PUMILUS
• Total number of polymer chains: 3
• Total formula weight: 41100.05

Authors

Sukackaite, R.,Grazulis, S.,Bochtler, M.,Siksnys, V. (deposition date: 2008-01-11, release date: 2008-05-06, Last modification date: 2024-05-08)

Primary citation

Sukackaite, R.,Grazulis, S.,Bochtler, M.,Siksnys, V.
The Recognition Domain of the Bpuji Restriction Endonuclease in Complex with Cognate DNA at 1.3-A Resolution.
J.Mol.Biol., 378:1084-, 2008

PubMed Abstract: Type IIS restriction endonucleases recognize asymmetric DNA sequences and cleave both DNA strands at fixed positions downstream of the recognition site. The restriction endonuclease BpuJI recognizes the asymmetric sequence 5'-CCCGT; however, it cuts at multiple sites in the vicinity of the target sequence. BpuJI consists of two physically separate domains, with catalytic and dimerization functions in the C-terminal domain and DNA recognition functions in the N-terminal domain. Here we report the crystal structure of the BpuJI recognition domain bound to cognate DNA at 1.3-A resolution. This region folds into two winged-helix subdomains, D1 and D2, interspaced by the DL subdomain. The D1 and D2 subdomains of BpuJI share structural similarity with the similar subdomains of the FokI DNA-binding domain; however, their orientations in protein-DNA complexes are different. Recognition of the 5'-CCCGT target sequence is achieved by BpuJI through the major groove contacts of amino acid residues located on both the helix-turn-helix motifs and the N-terminal arm. The role of these interactions in DNA recognition is also corroborated by mutational analysis.

PubMed: 18433771
DOI: 10.1016/J.JMB.2008.03.041

Experimental method

X-RAY DIFFRACTION (1.3 Å)