2g8h: Difference between revisions

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-[[Image:2g8h.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2g8h", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_2g8h|  PDB=2g8h  |  SCENE=  }}
-'''B. halodurans RNase H catalytic domain D192N mutant in complex with Mg2+ and RNA/DNA hybrid (non-P nick at the active site)'''
+==B. halodurans RNase H catalytic domain D192N mutant in complex with Mg2+ and RNA/DNA hybrid (non-P nick at the active site)==
+<StructureSection load='2g8h' size='340' side='right'caption='[[2g8h]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2g8h]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans Alkalihalobacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G8H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G8H 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]] 1.85&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</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=2g8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g8h OCA], [https://pdbe.org/2g8h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g8h RCSB], [https://www.ebi.ac.uk/pdbsum/2g8h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g8h ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</ref>
+== 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/g8/2g8h_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=2g8h ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In two-metal catalysis, metal ion A has been proposed to activate the nucleophile and metal ion B to stabilize the transition state. We recently reported crystal structures of RNase H-RNA/DNA substrate complexes obtained at 1.5-2.2 Angstroms. We have now determined and report here structures of reaction intermediate and product complexes of RNase H at 1.65-1.85 Angstroms. The movement of the two metal ions suggests how they may facilitate RNA hydrolysis during the catalytic process. Firstly, metal ion A may assist nucleophilic attack by moving towards metal ion B and bringing the nucleophile close to the scissile phosphate. Secondly, metal ion B transforms from an irregular coordination in the substrate complex to a more regular geometry in the product complex. The exquisite sensitivity of Mg(2+) to the coordination environment likely destabilizes the enzyme-substrate complex and reduces the energy barrier to form product. Lastly, product release probably requires dissociation of metal ion A, which is inhibited by either high concentrations of divalent cations or mutation of an assisting protein residue.
-==Overview==
+Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release.,Nowotny M, Yang W EMBO J. 2006 May 3;25(9):1924-33. Epub 2006 Apr 6. PMID:16601679<ref>PMID:16601679</ref>
-In two-metal catalysis, metal ion A has been proposed to activate the nucleophile and metal ion B to stabilize the transition state. We recently reported crystal structures of RNase H-RNA/DNA substrate complexes obtained at 1.5-2.2 Angstroms. We have now determined and report here structures of reaction intermediate and product complexes of RNase H at 1.65-1.85 Angstroms. The movement of the two metal ions suggests how they may facilitate RNA hydrolysis during the catalytic process. Firstly, metal ion A may assist nucleophilic attack by moving towards metal ion B and bringing the nucleophile close to the scissile phosphate. Secondly, metal ion B transforms from an irregular coordination in the substrate complex to a more regular geometry in the product complex. The exquisite sensitivity of Mg(2+) to the coordination environment likely destabilizes the enzyme-substrate complex and reduces the energy barrier to form product. Lastly, product release probably requires dissociation of metal ion A, which is inhibited by either high concentrations of divalent cations or mutation of an assisting protein residue.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-G8H is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G8H OCA].
+</div>
+<div class="pdbe-citations 2g8h" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release., Nowotny M, Yang W, EMBO J. 2006 May 3;25(9):1924-33. Epub 2006 Apr 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16601679 16601679]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-[[Category: Bacillus halodurans]]
+== References ==
-[[Category: Ribonuclease H]]
+<references/>
-[[Category: Single protein]]
+__TOC__
-[[Category: Nowotny, M.]]
+</StructureSection>
-[[Category: Yang, W.]]
+[[Category: Alkalihalobacillus halodurans]]
-[[Category: Ribonuclease h]]
+[[Category: Large Structures]]
-[[Category: Rna/dna hybrid]]
+[[Category: Nowotny M]]
-[[Category: Rnase h]]
+[[Category: Yang W]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 04:49:06 2008''