1E7D

Endonuclease VII (ENDOVII) Ffrom Phage T4

Summary for 1E7D

• Entry DOI: 10.2210/pdb1e7d/pdb
• Related: 1E7L 1EN7
• Descriptor: RECOMBINATION ENDONUCLEASE VII, ZINC ION, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: hydrolase, endonuclease, resolvase, holliday junction, dnase
• Biological source: BACTERIOPHAGE T4
• Total number of polymer chains: 2
• Total formula weight: 36664.89

Authors

Raaijmakers, H.C.A.,Vix, O.,Toro, I.,Suck, D. (deposition date: 2000-08-28, release date: 2001-05-04, Last modification date: 2023-12-13)

Primary citation

Raaijmakers, H.C.A.,Toro, I.,Birkenbihl, R.,Kemper, B.,Suck, D.
Conformational Flexibility in T4 Endonuclease Vii Revealed by Crystallography: Implications for Substrate Binding and Cleavage
J.Mol.Biol., 308:311-, 2001

PubMed Abstract: The structure of the N62D mutant of the junction-resolving endonuclease VII (EndoVII) from phage T4 has been refined at 1.3 A, and a second wild-type crystal form solved and refined at 2.8 A resolution. Comparison of the mutant with the wild-type protein structure in two different crystal environments reveals considerable conformational flexibility at the dimer level affecting the substrate-binding cleft, the dimerization interface and the orientation of the C-terminal domains. The opening of the DNA-binding cleft, the orientation of the C-terminal domains relative to the central dimerization domain as well as the relative positioning of helices in the dimerization interface appear to be sensitive to the crystal packing environment. The highly unexpected rearrangement within the extended hydrophobic interface does change the contact surface area but keeps the number of hydrophobic contacts about the same and will therefore not require significant energy input. The conformational flexibility most likely is of functional significance for the broad substrate specificity of EndoVII. Binding of sulphate ions in the mutant structure and their positions relative to the active-site metal ions and residues known to be essential for catalysis allows us to propose a possible catalytic mechanism. A comparison with the active-site geometries of other magnesium-dependent nucleases, among them the homing endonuclease I-PpoI and Serratia endonuclease, shows common features, suggesting related catalytic mechanisms.

PubMed: 11327769
DOI: 10.1006/JMBI.2001.4592

Experimental method

X-RAY DIFFRACTION (2.8 Å)