2qnc: Difference between revisions

Revision as of 15:14, 4 May 2008

Crystal structure of T4 Endonuclease VII N62D mutant in complex with a DNA Holliday junction

OverviewOverview

Holliday proposed a four-way DNA junction as an intermediate in homologous recombination, and such Holliday junctions have since been identified as a central component in DNA recombination and repair. Phage T4 endonuclease VII (endo VII) was the first enzyme shown to resolve Holliday junctions into duplex DNAs by introducing symmetrical nicks in equivalent strands. Several Holliday junction resolvases have since been characterized, but an atomic structure of a resolvase complex with a Holliday junction remained elusive. Here we report the crystal structure of an inactive T4 endo VII(N62D) complexed with an immobile four-way junction with alternating arm lengths of 10 and 14 base pairs. The junction is a hybrid of the conventional square-planar and stacked-X conformation. Endo VII protrudes into the junction point from the minor groove side, opening it to a 14 A x 32 A parallelogram. This interaction interrupts the coaxial stacking, yet every base pair surrounding the junction remains intact. Additional interactions involve the positively charged protein and DNA phosphate backbones. Each scissile phosphate that is two base pairs from the crossover interacts with a Mg2+ ion in the active site. The similar overall shape and surface charge potential of the Holliday junction resolvases endo VII, RuvC, Ydc2, Hjc and RecU, despite having different folds, active site composition and DNA sequence preference, suggest a conserved binding mode for Holliday junctions.

About this StructureAbout this Structure

2QNC is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.

ReferenceReference

Crystal structure of T4 endonuclease VII resolving a Holliday junction., Biertumpfel C, Yang W, Suck D, Nature. 2007 Oct 4;449(7162):616-20. Epub 2007 Sep 16. PMID:17873859 Page seeded by OCA on Sun May 4 15:14:23 2008

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OCA

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 [[Image:2qnc.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 2qnc |SIZE=350|CAPTION= <scene name='initialview01'>2qnc</scene>, resolution 3.10&Aring;
+The line below this paragraph, containing "STRUCTURE_2qnc", creates the "Structure Box" on the page.
-|SITE= <scene name='pdbsite=AC1:Zn+Binding+Site+For+Residue+A+158'>AC1</scene>, <scene name='pdbsite=AC2:Zn+Binding+Site+For+Residue+B+158'>AC2</scene>, <scene name='pdbsite=AC3:Mg+Binding+Site+For+Residue+A+159'>AC3</scene> and <scene name='pdbsite=AC4:Mg+Binding+Site+For+Residue+F+24'>AC4</scene>
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Crossover_junction_endodeoxyribonuclease Crossover junction endodeoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.22.4 3.1.22.4] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= 49 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])
+-->
-|DOMAIN=
+{{STRUCTURE_2qnc|  PDB=2qnc  |  SCENE=  }}
-|RELATEDENTRY=[[1e7d|1E7D]], [[1e7l|1E7L]], [[1en7|1EN7]], [[2qnf|2QNF]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qnc OCA], [http://www.ebi.ac.uk/pdbsum/2qnc PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2qnc RCSB]</span>
-}}
 '''Crystal structure of T4 Endonuclease VII N62D mutant in complex with a DNA Holliday junction'''
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 [[Category: Suck, D.]]
 [[Category: Yang, W.]]
-[[Category: alternative initiation]]
+[[Category: Alternative initiation]]
-[[Category: calcium]]
+[[Category: Calcium]]
-[[Category: endo vii]]
+[[Category: Endo vii]]
-[[Category: four-way junction]]
+[[Category: Four-way junction]]
-[[Category: holliday junction]]
+[[Category: Holliday junction]]
-[[Category: hydrolase]]
+[[Category: Hydrolase]]
-[[Category: hydrolase/dna complex]]
+[[Category: Hydrolase/dna complex]]
-[[Category: metal-binding]]
+[[Category: Metal-binding]]
-[[Category: resolvase]]
+[[Category: Resolvase]]
-[[Category: resolving-enzyme]]
+[[Category: Resolving-enzyme]]
-[[Category: t4 endonuclease vii]]
+[[Category: T4 endonuclease vii]]
-[[Category: zinc]]
+[[Category: Zinc]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 15:14:23 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:51:05 2008''