2g8h: Difference between revisions

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-[[Image:2g8h.png|left|200px]]
+==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 [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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G8H FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene><br>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1zbf|1zbf]], [[1zbi|1zbi]], [[1zbl|1zbl]], [[2g8f|2g8f]]</td></tr>
+<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rnhA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 Bacillus halodurans])</td></tr>
+<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g8h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g8h RCSB], [http://www.ebi.ac.uk/pdbsum/2g8h PDBsum]</span></td></tr>
+<table>
+== 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/chain_selection.php?pdb_ID=2ata 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.
-{{STRUCTURE_2g8h|  PDB=2g8h  |  SCENE=  }}
+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>
-===B. halodurans RNase H catalytic domain D192N mutant in complex with Mg2+ and RNA/DNA hybrid (non-P nick at the active site)===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_16601679}}
-==About this Structure==
-[[2g8h]] is a 3 chain structure with 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].
 ==See Also==
 *[[Ribonuclease|Ribonuclease]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:016601679</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Bacillus halodurans]]
 [[Category: Ribonuclease H]]