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[[Image:1e7d.gif|left|200px]]<br /><applet load="1e7d" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1e7d, resolution 2.80&Aring;" />
'''ENDONUCLEASE VII (ENDOVII) FROM PHAGE T4'''<br />


==Overview==
==Endonuclease VII (ENDOVII) Ffrom Phage T4==
<StructureSection load='1e7d' size='340' side='right'caption='[[1e7d]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1e7d]] is a 2 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=1E7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E7D 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]] 2.8&#8491;</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>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=1e7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e7d OCA], [https://pdbe.org/1e7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e7d RCSB], [https://www.ebi.ac.uk/pdbsum/1e7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e7d 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/e7/1e7d_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=1e7d ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The structure of the N62D mutant of the junction-resolving endonuclease VII (EndoVII) from phage T4 has been refined at 1.3 A, and a second wild-type crystal form solved and refined at 2.8 A resolution. Comparison of the mutant with the wild-type protein structure in two different crystal environments reveals considerable conformational flexibility at the dimer level affecting the substrate-binding cleft, the dimerization interface and the orientation of the C-terminal domains. The opening of the DNA-binding cleft, the orientation of the C-terminal domains relative to the central dimerization domain as well as the relative positioning of helices in the dimerization interface appear to be sensitive to the crystal packing environment. The highly unexpected rearrangement within the extended hydrophobic interface does change the contact surface area but keeps the number of hydrophobic contacts about the same and will therefore not require significant energy input. The conformational flexibility most likely is of functional significance for the broad substrate specificity of EndoVII. Binding of sulphate ions in the mutant structure and their positions relative to the active-site metal ions and residues known to be essential for catalysis allows us to propose a possible catalytic mechanism. A comparison with the active-site geometries of other magnesium-dependent nucleases, among them the homing endonuclease I-PpoI and Serratia endonuclease, shows common features, suggesting related catalytic mechanisms.
The structure of the N62D mutant of the junction-resolving endonuclease VII (EndoVII) from phage T4 has been refined at 1.3 A, and a second wild-type crystal form solved and refined at 2.8 A resolution. Comparison of the mutant with the wild-type protein structure in two different crystal environments reveals considerable conformational flexibility at the dimer level affecting the substrate-binding cleft, the dimerization interface and the orientation of the C-terminal domains. The opening of the DNA-binding cleft, the orientation of the C-terminal domains relative to the central dimerization domain as well as the relative positioning of helices in the dimerization interface appear to be sensitive to the crystal packing environment. The highly unexpected rearrangement within the extended hydrophobic interface does change the contact surface area but keeps the number of hydrophobic contacts about the same and will therefore not require significant energy input. The conformational flexibility most likely is of functional significance for the broad substrate specificity of EndoVII. Binding of sulphate ions in the mutant structure and their positions relative to the active-site metal ions and residues known to be essential for catalysis allows us to propose a possible catalytic mechanism. A comparison with the active-site geometries of other magnesium-dependent nucleases, among them the homing endonuclease I-PpoI and Serratia endonuclease, shows common features, suggesting related catalytic mechanisms.


==About this Structure==
Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage.,Raaijmakers H, Toro I, Birkenbihl R, Kemper B, Suck D J Mol Biol. 2001 Apr 27;308(2):311-23. PMID:11327769<ref>PMID:11327769</ref>
1E7D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t2 Enterobacteria phage t2] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=CL:'>CL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A+Putative+Active+Site+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Chain+B+Putative+Active+Site+Chain+B'>AC2</scene>, <scene name='pdbsite=AC3:Zn+Binding+Site+For+Chain+A'>AC3</scene> and <scene name='pdbsite=AC4:Zn+Binding+Site+For+Chain+B'>AC4</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E7D OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage., Raaijmakers H, Toro I, Birkenbihl R, Kemper B, Suck D, J Mol Biol. 2001 Apr 27;308(2):311-23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11327769 11327769]
</div>
[[Category: Enterobacteria phage t2]]
<div class="pdbe-citations 1e7d" style="background-color:#fffaf0;"></div>
[[Category: Single protein]]
[[Category: Raaijmakers, H C.A.]]
[[Category: Suck, D.]]
[[Category: Toro, I.]]
[[Category: Vix, O.]]
[[Category: CA]]
[[Category: CL]]
[[Category: ZN]]
[[Category: dnase]]
[[Category: endonuclease]]
[[Category: holliday junction]]
[[Category: hydrolase]]
[[Category: resolvase]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:24:40 2008''
==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia virus T4]]
[[Category: Large Structures]]
[[Category: Raaijmakers HCA]]
[[Category: Suck D]]
[[Category: Toro I]]
[[Category: Vix O]]

Latest revision as of 14:54, 13 December 2023

Endonuclease VII (ENDOVII) Ffrom Phage T4Endonuclease VII (ENDOVII) Ffrom Phage T4

Structural highlights

1e7d is a 2 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 2.8Å
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.

Publication Abstract from PubMed

The structure of the N62D mutant of the junction-resolving endonuclease VII (EndoVII) from phage T4 has been refined at 1.3 A, and a second wild-type crystal form solved and refined at 2.8 A resolution. Comparison of the mutant with the wild-type protein structure in two different crystal environments reveals considerable conformational flexibility at the dimer level affecting the substrate-binding cleft, the dimerization interface and the orientation of the C-terminal domains. The opening of the DNA-binding cleft, the orientation of the C-terminal domains relative to the central dimerization domain as well as the relative positioning of helices in the dimerization interface appear to be sensitive to the crystal packing environment. The highly unexpected rearrangement within the extended hydrophobic interface does change the contact surface area but keeps the number of hydrophobic contacts about the same and will therefore not require significant energy input. The conformational flexibility most likely is of functional significance for the broad substrate specificity of EndoVII. Binding of sulphate ions in the mutant structure and their positions relative to the active-site metal ions and residues known to be essential for catalysis allows us to propose a possible catalytic mechanism. A comparison with the active-site geometries of other magnesium-dependent nucleases, among them the homing endonuclease I-PpoI and Serratia endonuclease, shows common features, suggesting related catalytic mechanisms.

Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage.,Raaijmakers H, Toro I, Birkenbihl R, Kemper B, Suck D J Mol Biol. 2001 Apr 27;308(2):311-23. PMID:11327769[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. Raaijmakers H, Toro I, Birkenbihl R, Kemper B, Suck D. Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage. J Mol Biol. 2001 Apr 27;308(2):311-23. PMID:11327769 doi:10.1006/jmbi.2001.4592

1e7d, resolution 2.80Å

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