1G8T

SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT 1.1 A RESOLUTION

Summary for 1G8T

• Entry DOI: 10.2210/pdb1g8t/pdb
• Related: 1SMN
• Descriptor: NUCLEASE SM2 ISOFORM, SULFATE ION, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: endonuclease, hydrolase, nuclease, magnesium
• Biological source: Serratia marcescens
• Cellular location: Secreted: P13717
• Total number of polymer chains: 2
• Total formula weight: 53910.65

Authors

Lunin, V.V.,Perbandt, M.,Betzel, C.H.,Mikhailov, A.M. (deposition date: 2000-11-21, release date: 2000-12-06, Last modification date: 2024-12-25)

Primary citation

Shlyapnikov, S.V.,Lunin, V.V.,Perbandt, M.,Polyakov, K.M.,Lunin, V.Y.,Levdikov, V.M.,Betzel, C.,Mikhailov, A.M.
Atomic structure of the Serratia marcescens endonuclease at 1.1 A resolution and the enzyme reaction mechanism.
Acta Crystallogr.,Sect.D, 56:567-572, 2000

PubMed 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.

PubMed: 10771425
DOI: 10.1107/S090744490000322X

Experimental method

X-RAY DIFFRACTION (1.1 Å)