1F0O

PVUII ENDONUCLEASE/COGNATE DNA COMPLEX (GLUTARALDEHYDE-CROSSLINKED CRYSTAL) AT PH 7.5 WITH TWO CALCIUM IONS AT EACH ACTIVE SITE

Summary for 1F0O

• Entry DOI: 10.2210/pdb1f0o/pdb
• Related: 1EYU 1PVI 2PYI 3PYI
• Descriptor: (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C-3'), TYPE II RESTRICTION ENZYME PVUII, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: protein-dna complex, endonuclease type ii, restriction enzyme, catalytic metal visualization, hydrolase-dna complex, hydrolase/dna
• Biological source: Proteus vulgaris
• Total number of polymer chains: 4
• Total formula weight: 44837.47

Authors

Horton, J.R.,Cheng, X. (deposition date: 2000-05-16, release date: 2000-11-06, Last modification date: 2024-02-07)

Primary citation

Horton, J.R.,Cheng, X.
PvuII endonuclease contains two calcium ions in active sites.
J.Mol.Biol., 300:1049-1056, 2000

PubMed 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.

PubMed: 10903853
DOI: 10.1006/jmbi.2000.3938

Experimental method

X-RAY DIFFRACTION (2.5 Å)