1QL0

Sm Endonuclease from Seratia marcenscens at atomic resolution

Summary for 1QL0

• Entry DOI: 10.2210/pdb1ql0/pdb
• Related: 1SMN
• Descriptor: NUCLEASE, MAGNESIUM ION (3 entities in total)
• Functional Keywords: endonuclease, hydrolase, nuclease
• Biological source: SERRATIA MARCESCENS
• Total number of polymer chains: 2
• Total formula weight: 52639.63

Authors

Perbandt, M.,Mikhailov, A.M.,Betzel, C.H. (deposition date: 1999-08-18, release date: 2000-05-07, Last modification date: 2024-10-16)

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-, 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)