1m0d

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[[Image:1m0d.jpg|left|200px]]<br /><applet load="1m0d" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1m0d, resolution 1.90&Aring;" />
 
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'''Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions'''<br />
 
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==Overview==
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==Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions==
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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.
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<StructureSection load='1m0d' size='340' side='right'caption='[[1m0d]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1m0d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M0D FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1m0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0d OCA], [https://pdbe.org/1m0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m0d RCSB], [https://www.ebi.ac.uk/pdbsum/1m0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m0d ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ENDO_BPT7 ENDO_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:12628932</ref> <ref>PMID:23207296</ref> <ref>PMID:3972821</ref> <ref>PMID:9236119</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m0/1m0d_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m0d ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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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].
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
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==Reference==
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<references/>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12093751 12093751]
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__TOC__
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[[Category: Bacteriophage t7]]
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</StructureSection>
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[[Category: Deoxyribonuclease IV (phage-T(4)-induced)]]
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[[Category: Escherichia phage T7]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Declais, A C.]]
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[[Category: Declais AC]]
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[[Category: Hadden, J M.]]
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[[Category: Hadden JM]]
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[[Category: Lilley, D M.]]
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[[Category: Lilley DM]]
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[[Category: Phillips, S E.]]
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[[Category: Phillips SE]]
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[[Category: MN]]
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[[Category: SO4]]
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[[Category: composite active site]]
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[[Category: domain swapped]]
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[[Category: holliday junction resolvase]]
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[[Category: homodimer]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:50:12 2008''
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Current revision

Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions

PDB ID 1m0d

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