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New page: left|200px<br /><applet load="1m0d" size="450" color="white" frame="true" align="right" spinBox="true" caption="1m0d, resolution 1.90Å" /> '''Crystal Structure of...
 
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[[Image:1m0d.jpg|left|200px]]<br /><applet load="1m0d" size="450" color="white" frame="true" align="right" spinBox="true"
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'''Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions'''<br />


==Overview==
==Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions==
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.
<StructureSection load='1m0d' size='340' side='right'caption='[[1m0d]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
<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>
</table>
== Function ==
[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>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m0/1m0d_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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].
<div style="clear:both"></div>


==About this Structure==
==See Also==
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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1M0D OCA].
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 
== References ==
==Reference==
<references/>
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]
__TOC__
[[Category: Bacteriophage t7]]
</StructureSection>
[[Category: Deoxyribonuclease IV (phage-T(4)-induced)]]
[[Category: Escherichia phage T7]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Declais, A.C.]]
[[Category: Declais AC]]
[[Category: Hadden, J.M.]]
[[Category: Hadden JM]]
[[Category: Lilley, D.M.]]
[[Category: Lilley DM]]
[[Category: Phillips, S.E.]]
[[Category: Phillips SE]]
[[Category: MN]]
[[Category: SO4]]
[[Category: composite active site]]
[[Category: domain swapped]]
[[Category: holliday junction resolvase]]
[[Category: homodimer]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:01:51 2007''

Latest revision as of 10:38, 14 February 2024

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

Structural highlights

1m0d is a 4 chain structure with sequence from Escherichia phage T7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[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.

See Also

References

  1. ↑ Declais AC, Fogg JM, Freeman AD, Coste F, Hadden JM, Phillips SE, Lilley DM. The complex between a four-way DNA junction and T7 endonuclease I. EMBO J. 2003 Mar 17;22(6):1398-409. PMID:12628932 doi:http://dx.doi.org/10.1093/emboj/cdg132
  2. ↑ Freeman AD, Declais AC, Lilley DM. The importance of the N-terminus of T7 endonuclease I in the interaction with DNA junctions. J Mol Biol. 2013 Jan 23;425(2):395-410. doi: 10.1016/j.jmb.2012.11.029. Epub 2012, Dec 1. PMID:23207296 doi:http://dx.doi.org/10.1016/j.jmb.2012.11.029
  3. ↑ Panayotatos N, Fontaine A. An endonuclease specific for single-stranded DNA selectively damages the genomic DNA and induces the SOS response. J Biol Chem. 1985 Mar 10;260(5):3173-7. PMID:3972821
  4. ↑ Parkinson MJ, Lilley DM. The junction-resolving enzyme T7 endonuclease I: quaternary structure and interaction with DNA. J Mol Biol. 1997 Jul 11;270(2):169-78. PMID:9236119 doi:http://dx.doi.org/10.1006/jmbi.1997.1128

1m0d, resolution 1.90Å

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