2qnc: Difference between revisions

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New page: left|200px<br /><applet load="2qnc" size="350" color="white" frame="true" align="right" spinBox="true" caption="2qnc, resolution 3.10Å" /> '''Crystal structure of...
 
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[[Image:2qnc.jpg|left|200px]]<br /><applet load="2qnc" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2qnc, resolution 3.10&Aring;" />
'''Crystal structure of T4 Endonuclease VII N62D mutant in complex with a DNA Holliday junction'''<br />


==Overview==
==Crystal structure of T4 Endonuclease VII N62D mutant in complex with a DNA Holliday junction==
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.
<StructureSection load='2qnc' size='340' side='right'caption='[[2qnc]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2qnc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QNC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QNC 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]] 3.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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></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=2qnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qnc OCA], [https://pdbe.org/2qnc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qnc RCSB], [https://www.ebi.ac.uk/pdbsum/2qnc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qnc ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/END7_BPT4 END7_BPT4] Cleaves DNA cruciform and Y-structures as well as heteroduplex loops. Resolves Holliday junctions, recognizes a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches.
== 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/qn/2qnc_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=2qnc ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2QNC 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].
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17873859 17873859]
[[Category: Escherichia virus T4]]
[[Category: Crossover junction endodeoxyribonuclease]]
[[Category: Large Structures]]
[[Category: Pseudomonas phage d3112]]
[[Category: Biertumpfel C]]
[[Category: Single protein]]
[[Category: Suck D]]
[[Category: Biertumpfel, C.]]
[[Category: Yang W]]
[[Category: Suck, D.]]
[[Category: Yang, W.]]
[[Category: EDO]]
[[Category: MG]]
[[Category: ZN]]
[[Category: alternative initiation]]
[[Category: calcium]]
[[Category: endo vii]]
[[Category: four-way junction]]
[[Category: holliday junction]]
[[Category: hydrolase]]
[[Category: hydrolase/dna complex]]
[[Category: metal-binding]]
[[Category: resolvase]]
[[Category: resolving-enzyme]]
[[Category: t4 endonuclease vii]]
[[Category: zinc]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 31 10:59:06 2008''

Latest revision as of 12:17, 21 February 2024

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

Structural highlights

2qnc is a 6 chain structure with sequence from Escherichia virus T4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.1Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

END7_BPT4 Cleaves DNA cruciform and Y-structures as well as heteroduplex loops. Resolves Holliday junctions, recognizes a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2qnc, resolution 3.10Å

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