title: Atomic structure of the Serratia marcescens endonuclease at 1.1 A resolution and the enzyme reaction mechanism.
abstract: 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.
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 117984, Russia.
authors.forename: S V
authors.initials: SV
authors.lastname: Shlyapnikov
authors.forename: V V
authors.initials: VV
authors.lastname: Lunin
authors.forename: M
authors.initials: M
authors.lastname: Perbandt
authors.forename: K M
authors.initials: KM
authors.lastname: Polyakov
authors.forename: V Y
authors.initials: VY
authors.lastname: Lunin
authors.forename: V M
authors.initials: VM
authors.lastname: Levdikov
authors.forename: C
authors.initials: C
authors.lastname: Betzel
authors.forename: A M
authors.initials: AM
authors.lastname: Mikhailov
mesh_terms: 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
chemical_list: D013431:Sulfates; D014867:Water; D004706:Endodeoxyribonucleases; D004722:Endoribonucleases; C021835:Serratia marcescens nuclease; D008274:Magnesium