3E40

Q138F HincII bound to GTTAAC and cocrystallized with 5 mM Ca2+

Summary for 3E40

• Entry DOI: 10.2210/pdb3e40/pdb
• Related: 3E3Y 3E41 3E42 3E43 3E44 3E45
• Descriptor: Type-2 restriction enzyme HindII, 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DP*DAP*DAP*DCP*DCP*DGP*DGP*DC)-3'), CALCIUM ION, ... (5 entities in total)
• Functional Keywords: protein-dna complex, endonuclease, indirect readout, hydrolase, nuclease, restriction system, hydrolase-dna complex, hydrolase/dna
• Biological source: Haemophilus influenzae
• Total number of polymer chains: 4
• Total formula weight: 68390.90

Authors

Horton, N.C.,Babic, A.C.,Little, E.J.,Manohar, V.M. (deposition date: 2008-08-08, release date: 2008-08-26, Last modification date: 2024-02-21)

Primary citation

Babic, A.C.,Little, E.J.,Manohar, V.M.,Bitinaite, J.,Horton, N.C.
DNA distortion and specificity in a sequence-specific endonuclease.
J.Mol.Biol., 383:186-204, 2008

PubMed Abstract: Five new structures of the Q138F HincII enzyme bound to a total of three different DNA sequences and three different metal ions (Ca(2+), Mg(2+), and Mn(2+)) are presented. While previous structures were produced from soaking Ca(2+) into preformed Q138F HincII/DNA crystals, the new structures are derived from cocrystallization with Ca(2+), Mg(2+), or Mn(2+). The Mn(2)(+)-bound structure provides the first view of a product complex of Q138F HincII with cleaved DNA. Binding studies and a crystal structure show how Ca(2+) allows trapping of a Q138F HincII complex with noncognate DNA in a catalytically incompetent conformation. Many Q138F HincII/DNA structures show asymmetry, despite the binding of a symmetric substrate by a symmetric enzyme. The various complexes are fit into a model describing the different conformations of the DNA-bound enzyme and show how DNA conformational energetics determine DNA-cleavage rates by the Q138F HincII enzyme.

PubMed: 18762194
DOI: 10.1016/j.jmb.2008.08.032

Experimental method

X-RAY DIFFRACTION (2.1 Å)