1zbi: Difference between revisions
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New page: left|200px<br /><applet load="1zbi" size="450" color="white" frame="true" align="right" spinBox="true" caption="1zbi, resolution 1.85Å" /> '''Bacillus halodurans ... |
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== | ==Bacillus halodurans RNase H catalytic domain mutant D132N in complex with 12-mer RNA/DNA hybrid== | ||
RNase H belongs to a nucleotidyl-transferase superfamily, which includes | <StructureSection load='1zbi' size='340' side='right'caption='[[1zbi]], [[Resolution|resolution]] 1.85Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1zbi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans_C-125 Alkalihalobacillus halodurans C-125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZBI 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]] 1.85Å</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></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=1zbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zbi OCA], [https://pdbe.org/1zbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zbi RCSB], [https://www.ebi.ac.uk/pdbsum/1zbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zbi 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/zb/1zbi_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=1zbi ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
RNase H belongs to a nucleotidyl-transferase superfamily, which includes transposase, retroviral integrase, Holliday junction resolvase, and RISC nuclease Argonaute. We report the crystal structures of RNase H complexed with an RNA/DNA hybrid and a mechanism for substrate recognition and two-metal-ion-dependent catalysis. RNase H specifically recognizes the A form RNA strand and the B form DNA strand. Structure comparisons lead us to predict the catalytic residues of Argonaute and conclude that two-metal-ion catalysis is a general feature of the superfamily. In nucleases, the two metal ions are asymmetrically coordinated and have distinct roles in activating the nucleophile and stabilizing the transition state. In transposases, they are symmetrically coordinated and exchange roles to alternately activate a water and a 3'-OH for successive strand cleavage and transfer by a ping-pong mechanism. | |||
Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis.,Nowotny M, Gaidamakov SA, Crouch RJ, Yang W Cell. 2005 Jul 1;121(7):1005-16. PMID:15989951<ref>PMID:15989951</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1zbi" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Alkalihalobacillus halodurans C-125]] | |||
[[Category: Large Structures]] | |||
[[Category: Crouch RJ]] | |||
[[Category: Gaidamakov SA]] | |||
[[Category: Nowotny M]] | |||
[[Category: Yang W]] | |||
Latest revision as of 07:06, 23 August 2023
Bacillus halodurans RNase H catalytic domain mutant D132N in complex with 12-mer RNA/DNA hybrid
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