Title CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BPUJI RECOGNITION DOMAIN IN COMPLEX WITH COGNATE DNA 2vla_500
3D View: Jmol
Citation Bochtler, M., Grazulis, S., Siksnys, V., and Sukackaite, R. (2008), The Recognition Domain of the Bpuji Restriction Endonuclease in Complex with Cognate DNA at 1.3-A Resolution.. J.Mol.Biol. 378:1084-1093
[Abstract] [PubMed]
History Deposition: 2008-01-11
Experimental Method X-RAY DIFFRACTION , Resolution: 1.3 Å
Classification HYDROLASE
SCOP
Classification
Interface to Domain Species Protein Family Superfamily Fold Class
N/A [?]
Current SCOP release, 1.75 presumably does NOT classify the structure, 2VLA at the moment. Otherwise, there might be an error in the relation between SCOP entity and PDB structure entity of BIPA, please report us if you think this is the case.
Structural and Functional Restraints Polymer Sequence & Restraints
A
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MNYNPEEQFRCTIIRGKAKNMLDNLLPAYANIIDDICPCDKASFVKDFNNRLIEILGEETTKKTLDNHRTEIAGKLFGMFYEDDEVIFPSGRTNKYIEDSDQPAFFKDICFKFQFPNGMDKLDKVIEKVGAKIQIRQFPYILQVLLTADNNNIQLSKDDIAYYVLNSLQVLQGKIKPIEVIEKIIEDRSNDITKKVRHPGKETSYSMQHIREQLNYLELANLIRIDGNLVKLNYREAENINYIAQFWGNKPEFNAYKYDFTSEDDKKSFFKDWQQYYSNV
Key for HTML output
alpha helix red x
beta sheet blue x
positive phi italic x
solvent accessible upper case x
solvent inaccessible lower case x
disulfide bond cedilla ç
hydrogen bond to DNA orange background & bold x
water-mediated hydrogen bond to DNA orange background & overline x
van der Waals contact to DNA orange background & underline x
hydrogen bond to RNA cyan background & bold x
water-mediated hydrogen bond to RNA cyan background & overline x
van der Waals contact to RNA cyan background & underline x
binding to both DNA and RNA green background & bold x
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.
2vla_500
2VLA