2ixs

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[[Image:2ixs.gif|left|200px]]<br />
 
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<applet load="2ixs" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2ixs, resolution 2.00&Aring;" />
 
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'''STRUCTURE OF SDAI RESTRICTION ENDONUCLEASE'''<br />
 
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==Overview==
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==Structure of SdaI restriction endonuclease==
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Rare-cutting restriction enzymes are important tools in genome analysis., We report here the crystal structure of SdaI restriction endonuclease, which is specific for the 8 bp sequence CCTGCA/GG ("/" designates the, cleavage site). Unlike orthodox Type IIP enzymes, which are single domain, proteins, the SdaI monomer is composed of two structural domains. The N, domain contains a classical winged helix-turn-helix (wHTH) DNA binding, motif, while the C domain shows a typical restriction endonuclease fold., The active site of SdaI is located within the C domain and represents a, variant of the canonical PD-(D/E)XK motif. SdaI determinants of sequence, specificity are clustered on the recognition helix of the wHTH motif at, the N domain. The modular architecture of SdaI, wherein one domain, mediates DNA binding while the other domain is predicted to catalyze, hydrolysis, distinguishes SdaI from previously characterized restriction, enzymes interacting with symmetric recognition sequences.
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<StructureSection load='2ixs' size='340' side='right'caption='[[2ixs]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2ixs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_diastaticus Streptomyces diastaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IXS 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]] 2&#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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=2ixs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ixs OCA], [https://pdbe.org/2ixs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ixs RCSB], [https://www.ebi.ac.uk/pdbsum/2ixs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ixs ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/C4P954_STRDI C4P954_STRDI]
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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/ix/2ixs_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=2ixs ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Rare-cutting restriction enzymes are important tools in genome analysis. We report here the crystal structure of SdaI restriction endonuclease, which is specific for the 8 bp sequence CCTGCA/GG ("/" designates the cleavage site). Unlike orthodox Type IIP enzymes, which are single domain proteins, the SdaI monomer is composed of two structural domains. The N domain contains a classical winged helix-turn-helix (wHTH) DNA binding motif, while the C domain shows a typical restriction endonuclease fold. The active site of SdaI is located within the C domain and represents a variant of the canonical PD-(D/E)XK motif. SdaI determinants of sequence specificity are clustered on the recognition helix of the wHTH motif at the N domain. The modular architecture of SdaI, wherein one domain mediates DNA binding while the other domain is predicted to catalyze hydrolysis, distinguishes SdaI from previously characterized restriction enzymes interacting with symmetric recognition sequences.
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==About this Structure==
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The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture.,Tamulaitiene G, Jakubauskas A, Urbanke C, Huber R, Grazulis S, Siksnys V Structure. 2006 Sep;14(9):1389-400. PMID:16962970<ref>PMID:16962970</ref>
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2IXS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_diastaticus Streptomyces diastaticus] with SO4, EPE and TRS as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2IXS OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture., Tamulaitiene G, Jakubauskas A, Urbanke C, Huber R, Grazulis S, Siksnys V, Structure. 2006 Sep;14(9):1389-400. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16962970 16962970]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 2ixs" style="background-color:#fffaf0;"></div>
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[[Category: Streptomyces diastaticus]]
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[[Category: Type II site-specific deoxyribonuclease]]
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[[Category: Grazulis, S.]]
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[[Category: Huber, R.]]
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[[Category: Jakubauskas, A.]]
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[[Category: Siksnys, V.]]
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[[Category: Tamulaitiene, G.]]
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[[Category: Urbanke, C.]]
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[[Category: EPE]]
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[[Category: SO4]]
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[[Category: TRS]]
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[[Category: domain architecture]]
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[[Category: endonuclease]]
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[[Category: hydrolase]]
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[[Category: restriction endonuclease]]
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[[Category: sdai]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 14:20:54 2007''
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==See Also==
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Streptomyces diastaticus]]
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[[Category: Grazulis S]]
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[[Category: Huber R]]
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[[Category: Jakubauskas A]]
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[[Category: Siksnys V]]
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[[Category: Tamulaitiene G]]
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[[Category: Urbanke C]]

Current revision

Structure of SdaI restriction endonuclease

PDB ID 2ixs

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