1zbl

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:07, 23 August 2023) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1zbl.png|left|200px]]
 
-
{{STRUCTURE_1zbl| PDB=1zbl | SCENE= }}
+
==Bacillus halodurans RNase H catalytic domain mutant D192N in complex with 12-mer RNA/DNA hybrid==
 +
<StructureSection load='1zbl' size='340' side='right'caption='[[1zbl]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1zbl]] 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=1ZBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZBL 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]] 2.2&#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></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=1zbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zbl OCA], [https://pdbe.org/1zbl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zbl RCSB], [https://www.ebi.ac.uk/pdbsum/1zbl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zbl 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/1zbl_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=1zbl 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.
-
===Bacillus halodurans RNase H catalytic domain mutant D192N in complex with 12-mer RNA/DNA hybrid===
+
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>
-
{{ABSTRACT_PUBMED_15989951}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 1zbl" style="background-color:#fffaf0;"></div>
-
[[1zbl]] is a 4 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=1ZBL OCA].
+
==See Also==
==See Also==
-
*[[Ribonuclease|Ribonuclease]]
+
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:015989951</ref><references group="xtra"/>
+
__TOC__
-
[[Category: Bacillus halodurans]]
+
</StructureSection>
-
[[Category: Ribonuclease H]]
+
[[Category: Alkalihalobacillus halodurans C-125]]
-
[[Category: Crouch, R J.]]
+
[[Category: Large Structures]]
-
[[Category: Gaidamakov, S A.]]
+
[[Category: Crouch RJ]]
-
[[Category: Nowotny, M.]]
+
[[Category: Gaidamakov SA]]
-
[[Category: Yang, W.]]
+
[[Category: Nowotny M]]
-
[[Category: Dde motif]]
+
[[Category: Yang W]]
-
[[Category: Hydrolase-rna-dna complex]]
+
-
[[Category: Rna/dna hybrid]]
+
-
[[Category: Rnase h]]
+

Current revision

Bacillus halodurans RNase H catalytic domain mutant D192N in complex with 12-mer RNA/DNA hybrid

PDB ID 1zbl

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1zbl"
Personal tools