1e7d: Difference between revisions

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-{{Seed}}
-[[Image:1e7d.png|left|200px]]
-<!--
+==Endonuclease VII (ENDOVII) Ffrom Phage T4==
-The line below this paragraph, containing "STRUCTURE_1e7d", creates the "Structure Box" on the page.
+<StructureSection load='1e7d' size='340' side='right'caption='[[1e7d]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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>
-{{STRUCTURE_1e7d|  PDB=1e7d  |  SCENE=  }}
+<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.
-===ENDONUCLEASE VII (ENDOVII) FROM PHAGE T4===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1e7d" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11327769}}, adds the Publication Abstract to the page
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11327769 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11327769}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia virus T4]]
-E7D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E7D OCA].
+[[Category: Large Structures]]
+[[Category: Raaijmakers HCA]]
-==Reference==
+[[Category: Suck D]]
-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://www.ncbi.nlm.nih.gov/pubmed/11327769 11327769]
+[[Category: Toro I]]
-[[Category: Enterobacteria phage t4]]
+[[Category: Vix O]]
-[[Category: Single protein]]
-[[Category: Raaijmakers, H C.A.]]
-[[Category: Suck, D.]]
-[[Category: Toro, I.]]
-[[Category: Vix, O.]]
-[[Category: Dnase]]
-[[Category: Endonuclease]]
-[[Category: Holliday junction]]
-[[Category: Hydrolase]]
-[[Category: Resolvase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 00:16:32 2008''