1g8t
From Proteopedia
(New page: 200px<br /><applet load="1g8t" size="450" color="white" frame="true" align="right" spinBox="true" caption="1g8t, resolution 1.1Å" /> '''SM ENDONUCLEASE FROM ...) |
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| - | [[Image:1g8t.jpg|left|200px]]<br /><applet load="1g8t" size=" | + | [[Image:1g8t.jpg|left|200px]]<br /><applet load="1g8t" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1g8t, resolution 1.1Å" /> | caption="1g8t, resolution 1.1Å" /> | ||
'''SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT 1.1 A RESOLUTION'''<br /> | '''SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT 1.1 A RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The three-dimensional crystal structure of Serratia marcescens | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1G8T is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens] with SO4 and MG as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Serratia_marcescens_nuclease Serratia marcescens nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.30.2 3.1.30.2] Full crystallographic information is available from [http:// | + | 1G8T is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Serratia_marcescens_nuclease Serratia marcescens nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.30.2 3.1.30.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G8T OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Serratia marcescens nuclease]] | [[Category: Serratia marcescens nuclease]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Betzel, C | + | [[Category: Betzel, C H.]] |
| - | [[Category: Lunin, V | + | [[Category: Lunin, V V.]] |
| - | [[Category: Mikhailov, A | + | [[Category: Mikhailov, A M.]] |
[[Category: Perbandt, M.]] | [[Category: Perbandt, M.]] | ||
[[Category: MG]] | [[Category: MG]] | ||
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[[Category: signal]] | [[Category: signal]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:47:23 2008'' |
Revision as of 10:47, 21 February 2008
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SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT 1.1 A RESOLUTION
Overview
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.
About this Structure
1G8T is a Single protein structure of sequence from Serratia marcescens with and as ligands. Active as Serratia marcescens nuclease, with EC number 3.1.30.2 Full crystallographic information is available from OCA.
Reference
Atomic structure of the Serratia marcescens endonuclease at 1.1 A resolution and the enzyme reaction mechanism., Shlyapnikov SV, Lunin VV, Perbandt M, Polyakov KM, Lunin VY, Levdikov VM, Betzel C, Mikhailov AM, Acta Crystallogr D Biol Crystallogr. 2000 May;56(Pt 5):567-72. PMID:10771425
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