PDBsum entry 1ezh

Deoxyribonucleic acid

PDB id: 1ezh

Contents

DNA/RNA

Ligands

ECT

Theoretical model

PDB id:

1ezh

Name:

Deoxyribonucleic acid

Title:

Computer model of a covalent complex between d(taacggtta) and antitumor drug ecteinascidin 743

Structure:

DNA (5'-d( Tp Ap Ap Cp Gp Gp Tp Tp A)-3'). Chain: a. Engineered: yes. Other_details: covalent adduct between et743 and DNA. DNA (5'-d( Tp Ap Ap Cp Cp Gp Tp Tp A)-3'). Chain: b. Engineered: yes

Source:

Synthetic: yes. Synthetic: yes

Authors:

R.Garcia-Nieto,I.Manzanares,C.Cuevas,F.Gago

Key ref:

J.R.Horton and X.Cheng (2000). PvuII endonuclease contains two calcium ions in active sites. J Mol Biol, 300, 1049-1056. PubMed id: 10903853 DOI: 10.1006/jmbi.2000.3938

Date:

10-May-00 Release date: 22-May-00

DNA/RNA chains

T-A-A-C-G-G-T-T-A 9 bases

T-A-A-C-C-G-T-T-A 9 bases

DOI no: 10.1006/jmbi.2000.3938

J Mol Biol 300:1049-1056 (2000)

PubMed id: 10903853

PvuII endonuclease contains two calcium ions in active sites.

J.R.Horton, X.Cheng.

ABSTRACT

Restriction endonucleases differ in their use of metal cofactors despite having remarkably similar folds for their catalytic regions. To explore this, we have characterized the interaction of endonuclease PvuII with the catalytically incompetent cation Ca(2+). The structure of a glutaraldehyde-crosslinked crystal of the endonuclease PvuII-DNA complex, determined in the presence of Ca(2+) at a pH of approximately 6.5, supports a two-metal mechanism of DNA cleavage by PvuII. The first Ca(2+) position matches that found in all structurally examined endonucleases, while the second position is similar to that of EcoRV but is distinct from that of BamHI and BglI. The location of the second metal in PvuII, unlike that in BamHI/BglI, permits no direct interaction between the second metal and the O3' oxygen leaving group. However, the interactions between the DNA scissile phosphate and the metals, the first metal and the attacking water, and the attacking water and DNA are the same in PvuII as they are in the two-metal models of BamHI and BglI, but are distinct from the proposed three-metal or the two-metal models of EcoRV.

Selected figure(s)

Figure 1.
Figure 1. The primed active site of homodimeric PvuII-DNA complexes: (a) PvuII D34G mutant at pH 4.5 (pdb 3PVI; [Horton et al 1998b]), (b) PvuII at pH 4.5 in the presence of calcium (pdb 1EYU), and (c) crosslinked PvuII at pH 6.5 in the presence of calcium (pdb 1F0O). The calcium ions are labeled I and II and water molecules are labeled a, b, c in white lettering. Amino acid and nucleic acid residues are labeled with black lettering. The difference F[o] -F[c] electron density, contoured at 4.5s (green) and 8s (red) levels, illustrates the position of omitted water molecules and calcium ions. Arrows indicate the scissile bond.

Figure 2.
Figure 2. The octahedral coordination of two Ca^2+ observed in PvuII-DNA-Ca^2+ interactions. The numbers indicate the distance in Å between interacting atoms. Ca^2+ at site I has six coordination ligands including the attacking water (labeled a), and Ca^2+ at site II has five including the protonating water (labeled p), respectively.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 300, 1049-1056) copyright 2000.

Figures were selected by the author.