PvuII-endonuclease induces structural alterations at the scissile phosphate group of its cognate DNA.
We investigated the PvuII endonuclease with its cognate DNA by means of molecular dynamics simulations. Comparing the complexed DNA with a reference simulation of free DNA, we saw structural changes at the scissile phosphodiester bond. At this GpC step, the enzyme induces the highest twist and axial rise, inclination is increased and the minor groove widened. The distance between the scissile phosphate group and the phosphate group of the following thymine base is shortened significantly, indicating a substrate-assisted catalysis. A feasible reason for this vicinity is the catalytically important amino acid residue lysine 70, which bridges the free oxygen atoms of the successive phosphate groups. Due to this geometry, a compact reaction pocket is formed where a water molecule can be held, thus bringing the reaction partners for hydrolysis into contact. The O1-P-O2 angle of the scissile nucleotide is decreased, probably due to a complexation of the negative oxygen atoms through protein and solvent contacts.
Rauch
Christine
C
Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020, Innsbruck, Austria.
Trieb
Michael
M
Flader
Wolfgang
W
Wellenzohn
Bernd
B
Winger
Rudolf H
RH
Mayer
Erwin
E
Hallbrucker
Andreas
A
Liedl
Klaus R
KR
D001665:Binding Sites; D002118:Calcium / Q000378:metabolism; D020134:Catalytic Domain; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry* / Q000378:metabolism*; D008274:Magnesium / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010710:Phosphates / Q000737:chemistry*; D040681:Structural Homology, Protein; D014867:Water
D010710:Phosphates; D014867:Water; D004247:DNA; C061224:endodeoxyribonuclease PvuI; D015252:Deoxyribonucleases, Type II Site-Specific; D008274:Magnesium; D002118:Calcium