Atomic structure of the Serratia marcescens endonuclease at 1.1 A resolution and the enzyme reaction mechanism.
The three-dimensional crystal structure of Serratia marcescens endonuclease has been refined at 1.1 A resolution to an R factor of 12.9% and an R(free) of 15.6% with the use of anisotropic temperature factors. The model contains 3694 non-H atoms, 715 water molecules, four sulfate ions and two Mg(2+)-binding sites at the active sites of the homodimeric protein. It is shown that the magnesium ion linked to the active-site Asn119 of each monomer is surrounded by five water molecules and shows an octahedral coordination geometry. The temperature factors for the bound Mg(2+) ions in the A and B subunits are 7.08 and 4.60 A(2), respectively, and the average temperature factors for the surrounding water molecules are 12.13 and 10.3 A(2), respectively. In comparison with earlier structures, alternative side-chain conformations are defined for 51 residues of the dimer, including the essential active-site residue Arg57. A plausible mechanism of enzyme function is proposed based on the high-resolution S. marcescens nuclease structure, the functional characteristics of the natural and mutational forms of the enzyme and consideration of its structural analogy with homing endo-nuclease I-PpoI.
Shlyapnikov
S V
SV
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 117984, Russia.
Lunin
V V
VV
Perbandt
M
M
Polyakov
K M
KM
Lunin
V Y
VY
Levdikov
V M
VM
Betzel
C
C
Mikhailov
A M
AM
D001665:Binding Sites; D003196:Computer Graphics; D018360:Crystallography, X-Ray; D019281:Dimerization; D004706:Endodeoxyribonucleases / Q000737:chemistry* / Q000378:metabolism*; D004722:Endoribonucleases / Q000737:chemistry* / Q000378:metabolism*; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D012706:Serratia marcescens / Q000201:enzymology*; D013431:Sulfates / Q000378:metabolism; D014867:Water
D013431:Sulfates; D014867:Water; D004706:Endodeoxyribonucleases; D004722:Endoribonucleases; C021835:Serratia marcescens nuclease; D008274:Magnesium