1m0i: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1m0i]] is a 4 chain structure with 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=1M0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M0I FirstGlance]. <br> | <table><tr><td colspan='2'>[[1m0i]] is a 4 chain structure with 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=1M0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M0I FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>< | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fzr|1fzr]], [[1m0d|1m0d]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fzr|1fzr]], [[1m0d|1m0d]]</td></tr> | ||
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 Enterobacteria phage T7])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 Enterobacteria phage T7])</td></tr> | ||
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr> | ||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m0i RCSB], [http://www.ebi.ac.uk/pdbsum/1m0i PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m0i RCSB], [http://www.ebi.ac.uk/pdbsum/1m0i PDBsum]</span></td></tr> | ||
<table> | </table> | ||
== Function == | |||
[[http://www.uniprot.org/uniprot/ENRN_BPT7 ENRN_BPT7]] Junction-resolving enzyme that selectively binds and cleaves four-way (Holliday) DNA junctions present after viral genomic replication. These intermediates are created during DNA repair, processing of stalled replication forks and homologous genetic recombination. Introduces two nicks on the two non-crossing strands, at 5' sides of the junction. Participates also together with gp6 in the degradation of host chromosome to provide nucleotides for phage DNA synthesis.<ref>PMID:3972821</ref> <ref>PMID:9236119</ref> <ref>PMID:12628932</ref> <ref>PMID:23207296</ref> | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Enterobacteria phage t7]] | [[Category: Enterobacteria phage t7]] | ||
[[Category: Declais, A C | [[Category: Declais, A C]] | ||
[[Category: Hadden, J M | [[Category: Hadden, J M]] | ||
[[Category: Lilley, D M | [[Category: Lilley, D M]] | ||
[[Category: Phillips, S E | [[Category: Phillips, S E]] | ||
[[Category: Composite active site]] | [[Category: Composite active site]] | ||
[[Category: Domain swapped]] | [[Category: Domain swapped]] | ||
Revision as of 14:24, 25 December 2014
Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active SiteCrystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site
Structural highlights
Function[ENRN_BPT7] Junction-resolving enzyme that selectively binds and cleaves four-way (Holliday) DNA junctions present after viral genomic replication. These intermediates are created during DNA repair, processing of stalled replication forks and homologous genetic recombination. Introduces two nicks on the two non-crossing strands, at 5' sides of the junction. Participates also together with gp6 in the degradation of host chromosome to provide nucleotides for phage DNA synthesis.[1] [2] [3] [4] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedT7 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. 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[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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