1m0d
From Proteopedia
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|PDB= 1m0d |SIZE=350|CAPTION= <scene name='initialview01'>1m0d</scene>, resolution 1.90Å | |PDB= 1m0d |SIZE=350|CAPTION= <scene name='initialview01'>1m0d</scene>, resolution 1.90Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene> | + | |LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
| - | |GENE= Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | + | |GENE= Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 Enterobacteria phage T7]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1fzr|1FZR]], [[1m0i|1M0I]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0d OCA], [http://www.ebi.ac.uk/pdbsum/1m0d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1m0d RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1M0D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 1M0D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0D OCA]. |
==Reference== | ==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:[http://www.ncbi.nlm.nih.gov/pubmed/12093751 12093751] | 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:[http://www.ncbi.nlm.nih.gov/pubmed/12093751 12093751] | ||
| - | [[Category: Bacteriophage t7]] | ||
[[Category: Deoxyribonuclease IV (phage-T(4)-induced)]] | [[Category: Deoxyribonuclease IV (phage-T(4)-induced)]] | ||
| + | [[Category: Enterobacteria phage t7]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Declais, A C.]] | [[Category: Declais, A C.]] | ||
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[[Category: Lilley, D M.]] | [[Category: Lilley, D M.]] | ||
[[Category: Phillips, S E.]] | [[Category: Phillips, S E.]] | ||
| - | [[Category: MN]] | ||
| - | [[Category: SO4]] | ||
[[Category: composite active site]] | [[Category: composite active site]] | ||
[[Category: domain swapped]] | [[Category: domain swapped]] | ||
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[[Category: homodimer]] | [[Category: homodimer]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:09:40 2008'' |
Revision as of 19:09, 30 March 2008
| |||||||
| , resolution 1.90Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | Endonuclease I (Enterobacteria phage T7) | ||||||
| Activity: | Deoxyribonuclease IV (phage-T(4)-induced), with EC number 3.1.21.2 | ||||||
| Related: | 1FZR, 1M0I
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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 Enterobacteria phage t7. 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 Sun Mar 30 22:09:40 2008
