PDBsum entry 1rv5

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Hydrolase/DNA PDB id
Protein chains
240 a.a.
227 a.a.
Waters ×492

References listed in PDB file
Key reference
Title Role of protein-Induced bending in the specificity of DNA recognition: crystal structure of ecorv endonuclease complexed with d(aaagat) + d(atctt).
Authors N.C.Horton, J.J.Perona.
Ref. J Mol Biol, 1998, 277, 779-787. [DOI no: 10.1006/jmbi.1998.1655]
PubMed id 9545372
The crystal structure of EcoRV endonuclease has been determined at 2. 1 A resolution complexed to two five-base-pair DNA duplexes each containing the cognate recognition half-site. The highly localized 50 degrees bend into the major groove seen at the center TA-step of the continuous GATATC site is preserved in this discontinuous DNA complex lacking the scissile phosphates. Thus, this crystal structure provides evidence that covalent constraints associated with a continuous target site are not essential to enzyme-induced DNA bending, even when these constraints are removed directly at the locus of the bend. The scissile phosphates are also absent in the crystal structure of EcoRV bound to the non-specific site TCGCGA, which shows a straight B-like conformation. We conclude that DNA bending by EcoRV is governed only by the sequence and is not influenced by the continuity of the phosphodiester backbone. Together with other data showing that cleavable non-cognate sites are bent, these results indicate that EcoRV bends non-cognate sites differing by one or two base-pairs from GATATC, but does not bend non-specific sites that are less similar. Structural and thermodynamic considerations suggest that the sequence-dependent energy cost of DNA bending is likely to play an important role in determining the specificity of EcoRV. This differential cost is manifested at the binding step for bent non-cognate sequences and at the catalytic step for unbent non-specific sequences.
Figure 1.
Figure 1. A, Crystal structure of EcoRV bound to the specific DNA undecamer 5′-AAAGATATCTT [Kostrewa and Winkler 1995]. B, Crystal structure of EcoRV bound to two non-specific DNA octamers CGAGCTCG [Winkler et al 1993], in which the two octamers are stacked end-to-end with phosphates in the scissile position missing. C, Crystal structure of EcoRV complexed with the two duplexes d(AAAGAT) + d(ATCTT), also with the scissile phosphates missing (Table 1). The helical axes of the DNA are indicated by the continuous black lines in each case.
Figure 3.
Figure 3. Stereo view of the EcoRV-DNA specific DNA complex (blue), the product complex (green) and the discontinuous specific co-crystal structure lacking the scissile phosphates (red), at the center TA step of the recognition site. Cross-strand stacking of A7 of GATATC from each strand of the DNA duplex in the product complex (green) can be seen at center.
The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 277, 779-787) copyright 1998.
Secondary reference #1
Title The crystal structure of ecorv endonuclease and of its complexes with cognate and non-Cognate DNA fragments.
Authors F.K.Winkler, D.W.Banner, C.Oefner, D.Tsernoglou, R.S.Brown, S.P.Heathman, R.K.Bryan, P.D.Martin, K.Petratos, K.S.Wilson.
Ref. Embo J, 1993, 12, 1781-1795.
PubMed id 8491171
Secondary reference #2
Title Structure and function of restriction endonucleases
Author F.K.Winkler.
Ref. curr opin struct biol, 1992, 2, 93.
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