1zbf

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(New page: 200px<br /><applet load="1zbf" size="450" color="white" frame="true" align="right" spinBox="true" caption="1zbf, resolution 1.50&Aring;" /> '''Crystal structure of...)
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[[Image:1zbf.gif|left|200px]]<br /><applet load="1zbf" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1zbf, resolution 1.50&Aring;" />
 
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'''Crystal structure of B. halodurans RNase H catalytic domain mutant D132N'''<br />
 
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==Overview==
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==Crystal structure of B. halodurans RNase H catalytic domain mutant D132N==
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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.
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<StructureSection load='1zbf' size='340' side='right'caption='[[1zbf]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1zbf]] is a 1 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=1ZBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZBF FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zbf OCA], [https://pdbe.org/1zbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zbf RCSB], [https://www.ebi.ac.uk/pdbsum/1zbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zbf ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zb/1zbf_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1zbf ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1ZBF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ZBF OCA].
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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== References ==
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==Reference==
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<references/>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15989951 15989951]
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__TOC__
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[[Category: Bacillus halodurans]]
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</StructureSection>
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[[Category: Ribonuclease H]]
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[[Category: Alkalihalobacillus halodurans C-125]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Crouch, R.J.]]
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[[Category: Crouch RJ]]
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[[Category: Gaidamakov, S.A.]]
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[[Category: Gaidamakov SA]]
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[[Category: Nowotny, M.]]
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[[Category: Nowotny M]]
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[[Category: Yang, W.]]
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[[Category: Yang W]]
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[[Category: SO4]]
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[[Category: dde motif]]
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[[Category: rna/dna hybrid]]
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[[Category: rnase h]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:21:56 2007''
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Current revision

Crystal structure of B. halodurans RNase H catalytic domain mutant D132N

PDB ID 1zbf

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