2qnc: Difference between revisions

Revision as of 19:40, 21 February 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 Pseudomonas phage d3112 with , and as ligands. Active as Crossover junction endodeoxyribonuclease, with EC number 3.1.22.4 Known structural/functional Sites: , , and . 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

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 ==Overview==
-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.
+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 Structure==
-QNC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_phage_d3112 Pseudomonas phage d3112] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Known structural/functional Sites: <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>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QNC OCA].
+QNC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_phage_d3112 Pseudomonas phage d3112] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Known structural/functional Sites: <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>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QNC OCA].
 ==Reference==
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 [[Category: zinc]]
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