1m0d
From Proteopedia
(New page: 200px<br /><applet load="1m0d" size="450" color="white" frame="true" align="right" spinBox="true" caption="1m0d, resolution 1.90Å" /> '''Crystal Structure of...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1m0d.jpg|left|200px]]<br /><applet load="1m0d" size=" | + | [[Image:1m0d.jpg|left|200px]]<br /><applet load="1m0d" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1m0d, resolution 1.90Å" /> | caption="1m0d, resolution 1.90Å" /> | ||
'''Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions'''<br /> | '''Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions'''<br /> | ||
==Overview== | ==Overview== | ||
| - | T7 endonuclease I is a nuclease that is selective for the structure of the | + | T7 endonuclease I is a nuclease that is selective for the structure of the four-way DNA junction. The active site is similar to those of a number of restriction enzymes. We have solved the crystal structure of endonuclease I with a wild-type active site. Diffusion of manganese ions into the crystal revealed two peaks of electron density per active site, defining two metal ion-binding sites. Site 1 is fully occupied, and the manganese ion is coordinated by the carboxylate groups of Asp55 and Glu65, and the main chain carbonyl of Thr66. Site 2 is partially occupied, and the metal ion has a single protein ligand, the remaining carboxylate oxygen atom of Asp55. Isothermal titration calorimetry showed the sequential exothermic binding of two manganese ions in solution, with dissociation constants of 0.58 +/- 0.019 and 14 +/- 1.5 mM. These results are consistent with a two metal ion mechanism for the cleavage reaction, in which the hydrolytic water molecule is contained in the first coordination sphere of the site 1-bound metal ion. |
==About this Structure== | ==About this Structure== | ||
| - | 1M0D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t7 Bacteriophage t7] with MN and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] Full crystallographic information is available from [http:// | + | 1M0D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t7 Bacteriophage t7] with <scene name='pdbligand=MN:'>MN</scene> and <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0D OCA]. |
==Reference== | ==Reference== | ||
| Line 14: | Line 14: | ||
[[Category: Deoxyribonuclease IV (phage-T(4)-induced)]] | [[Category: Deoxyribonuclease IV (phage-T(4)-induced)]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Declais, A | + | [[Category: Declais, A C.]] |
| - | [[Category: Hadden, J | + | [[Category: Hadden, J M.]] |
| - | [[Category: Lilley, D | + | [[Category: Lilley, D M.]] |
| - | [[Category: Phillips, S | + | [[Category: Phillips, S E.]] |
[[Category: MN]] | [[Category: MN]] | ||
[[Category: SO4]] | [[Category: SO4]] | ||
| Line 25: | Line 25: | ||
[[Category: homodimer]] | [[Category: homodimer]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:50:12 2008'' |
Revision as of 11:50, 21 February 2008
|
Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions
Overview
T7 endonuclease I is a nuclease that is selective for the structure of the four-way DNA junction. The active site is similar to those of a number of restriction enzymes. We have solved the crystal structure of endonuclease I with a wild-type active site. Diffusion of manganese ions into the crystal revealed two peaks of electron density per active site, defining two metal ion-binding sites. Site 1 is fully occupied, and the manganese ion is coordinated by the carboxylate groups of Asp55 and Glu65, and the main chain carbonyl of Thr66. Site 2 is partially occupied, and the metal ion has a single protein ligand, the remaining carboxylate oxygen atom of Asp55. Isothermal titration calorimetry showed the sequential exothermic binding of two manganese ions in solution, with dissociation constants of 0.58 +/- 0.019 and 14 +/- 1.5 mM. These results are consistent with a two metal ion mechanism for the cleavage reaction, in which the hydrolytic water molecule is contained in the first coordination sphere of the site 1-bound metal ion.
About this Structure
1M0D is a Single protein structure of sequence from Bacteriophage t7 with and as ligands. Active as Deoxyribonuclease IV (phage-T(4)-induced), with EC number 3.1.21.2 Full crystallographic information is available from OCA.
Reference
Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I., Hadden JM, Declais AC, Phillips SE, Lilley DM, EMBO J. 2002 Jul 1;21(13):3505-15. PMID:12093751
Page seeded by OCA on Thu Feb 21 13:50:12 2008
