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| | <StructureSection load='2pfj' size='340' side='right'caption='[[2pfj]], [[Resolution|resolution]] 3.10Å' scene=''> | | <StructureSection load='2pfj' size='340' side='right'caption='[[2pfj]], [[Resolution|resolution]] 3.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2pfj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt7 Bpt7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PFJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PFJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2pfj]] 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=2PFJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PFJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fzr|1fzr]], [[1m0d|1m0d]], [[1m0i|1m0i]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 BPT7])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </span></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=2pfj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pfj OCA], [https://pdbe.org/2pfj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pfj RCSB], [https://www.ebi.ac.uk/pdbsum/2pfj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pfj ProSAT]</span></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=2pfj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pfj OCA], [https://pdbe.org/2pfj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pfj RCSB], [https://www.ebi.ac.uk/pdbsum/2pfj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pfj ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == 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>
| + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bpt7]] | + | [[Category: Escherichia phage T7]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Carr, S B]] | + | [[Category: Carr SB]] |
| - | [[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: Composite active site]]
| + | |
| - | [[Category: Domain swapped]]
| + | |
| - | [[Category: Holliday junction resolvase]]
| + | |
| - | [[Category: Homodimer]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Hydrolase-dna complex]]
| + | |
| Structural highlights
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.
Publication Abstract from PubMed
The four-way (Holliday) DNA junction is the central intermediate in homologous recombination, a ubiquitous process that is important in DNA repair and generation of genetic diversity. The penultimate stage of recombination requires resolution of the DNA junction into nicked-duplex species by the action of a junction-resolving enzyme, examples of which have been identified in a wide variety of organisms. These enzymes are nucleases that are highly selective for the structure of branched DNA. The mechanism of this selectivity has, however, been unclear in the absence of structural data. Here we present the crystal structure of the junction-resolving enzyme phage T7 endonuclease I in complex with a synthetic four-way DNA junction. Although the enzyme is structure-selective, significant induced fit occurs in the interaction, with changes in the structure of both the protein and the junction. The dimeric enzyme presents two binding channels that contact the backbones of the junction's helical arms over seven nucleotides. These interactions effectively measure the relative orientations and positions of the arms of the junction, thereby ensuring that binding is selective for branched DNA that can achieve this geometry.
The structural basis of Holliday junction resolution by T7 endonuclease I.,Hadden JM, Declais AC, Carr SB, Lilley DM, Phillips SE Nature. 2007 Oct 4;449(7162):621-4. Epub 2007 Sep 16. PMID:17873858[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ Hadden JM, Declais AC, Carr SB, Lilley DM, Phillips SE. The structural basis of Holliday junction resolution by T7 endonuclease I. Nature. 2007 Oct 4;449(7162):621-4. Epub 2007 Sep 16. PMID:17873858 doi:10.1038/nature06158
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