1nzb: Difference between revisions
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|PDB= 1nzb |SIZE=350|CAPTION= <scene name='initialview01'>1nzb</scene>, resolution 3.10Å | |PDB= 1nzb |SIZE=350|CAPTION= <scene name='initialview01'>1nzb</scene>, resolution 3.10Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene> | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UMP:2'-DEOXYURIDINE+5'-MONOPHOSPHATE'>UMP</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1ouq|1OUQ]], [[1q3u|1Q3U]], [[1q3v|1Q3V]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nzb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzb OCA], [http://www.ebi.ac.uk/pdbsum/1nzb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nzb RCSB]</span> | |||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
1NZB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | 1NZB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_p1 Enterobacteria phage p1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZB OCA]. | ||
==Reference== | ==Reference== | ||
Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation., Ennifar E, Meyer JE, Buchholz F, Stewart AF, Suck D, Nucleic Acids Res. 2003 Sep 15;31(18):5449-60. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12954782 12954782] | Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation., Ennifar E, Meyer JE, Buchholz F, Stewart AF, Suck D, Nucleic Acids Res. 2003 Sep 15;31(18):5449-60. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12954782 12954782] | ||
[[Category: Enterobacteria phage | [[Category: Enterobacteria phage p1]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Buchholz, F.]] | [[Category: Buchholz, F.]] | ||
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[[Category: Stewart, A F.]] | [[Category: Stewart, A F.]] | ||
[[Category: Suck, D.]] | [[Category: Suck, D.]] | ||
[[Category: cre]] | [[Category: cre]] | ||
[[Category: dna]] | [[Category: dna]] | ||
[[Category: recombinase]] | [[Category: recombinase]] | ||
''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 22:37:35 2008'' | ||
Revision as of 22:37, 30 March 2008
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| , resolution 3.10Å | |||||||
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| Ligands: | , , , , , , | ||||||
| Related: | 1OUQ, 1Q3U, 1Q3V
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of wild type Cre recombinase-loxP synapse
OverviewOverview
Escherichia coli phage P1 Cre recombinase catalyzes the site-specific recombination of DNA containing loxP sites. We report here two crystal structures of a wild-type Cre recombinase-loxP synaptic complex corresponding to two distinct reaction states: an initial pre-cleavage complex, trapped using a phosphorothioate modification at the cleavable scissile bond that prevents the recombination reaction, and a 3'-phosphotyrosine protein-DNA intermediate resulting from the first strand cleavage. In contrast to previously determined Cre complexes, both structures contain a full tetrameric complex in the asymmetric unit, unequivocally showing that the anti-parallel arrangement of the loxP sites is an intrinsic property of the Cre-loxP recombination synapse. The conformation of the spacer is different to the one observed for the symmetrized loxS site: a kink next to the scissile phosphate in the top strand of the pre-cleavage complex leads to unstacking of the TpG step and a widening of the minor groove. This side of the spacer is interacting with a 'cleavage-competent' Cre subunit, suggesting that the first cleavage occurs at the ApT step in the top strand. This is further confirmed by the structure of the 3'-phosphotyrosine intermediate, where the DNA is cleaved in the top strands and covalently linked to the 'cleavage-competent' subunits. The cleavage is followed by a movement of the C-terminal part containing the attacking Y324 and the helix N interacting with the 'non-cleaving' subunit. This rearrangement could be responsible for the interconversion of Cre subunits. Our results also suggest that the Cre-induced kink next to the scissile phosphodiester activates the DNA for cleavage at this position and facilitates strand transfer.
About this StructureAbout this Structure
1NZB is a Single protein structure of sequence from Enterobacteria phage p1. Full crystallographic information is available from OCA.
ReferenceReference
Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation., Ennifar E, Meyer JE, Buchholz F, Stewart AF, Suck D, Nucleic Acids Res. 2003 Sep 15;31(18):5449-60. PMID:12954782
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