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| | ==Selenium Derivatized RNA/DNA Hybrid in complex with RNase H Catalytic Domain D132N Mutant== | | ==Selenium Derivatized RNA/DNA Hybrid in complex with RNase H Catalytic Domain D132N Mutant== |
| - | <StructureSection load='3twh' size='340' side='right' caption='[[3twh]], [[Resolution|resolution]] 1.79Å' scene=''> | + | <StructureSection load='3twh' size='340' side='right'caption='[[3twh]], [[Resolution|resolution]] 1.79Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3twh]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_alcalophilus_subsp._halodurans"_boyer_et_al._1973 "bacillus alcalophilus subsp. halodurans" boyer et al. 1973]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TWH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TWH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3twh]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans Alkalihalobacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TWH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TWH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.79Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SDG:2-AMINO-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURINE-6-SELENOL'>SDG</scene></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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SDG:2-AMINO-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURINE-6-SELENOL'>SDG</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1zbi|1zbi]], [[2g8u|2g8u]]</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=3twh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3twh OCA], [https://pdbe.org/3twh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3twh RCSB], [https://www.ebi.ac.uk/pdbsum/3twh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3twh ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BH0863, rnhA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 "Bacillus alcalophilus subsp. halodurans" Boyer et al. 1973])</td></tr>
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| - | <tr id='activity'><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>
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3twh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3twh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3twh RCSB], [http://www.ebi.ac.uk/pdbsum/3twh PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. | + | [https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</ref> |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | The crystal structures of protein-nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein-nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H-RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.
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| - | Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides.,Abdur R, Gerlits OO, Gan J, Jiang J, Salon J, Kovalevsky AY, Chumanevich AA, Weber IT, Huang Z Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):354-61. doi:, 10.1107/S1399004713027922. Epub 2014 Jan 29. PMID:24531469<ref>PMID:24531469</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| | ==See Also== | | ==See Also== |
| - | *[[Ribonuclease|Ribonuclease]] | + | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] |
| - | *[[Temp|Temp]]
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| - | *[[User:Jaime.Prilusky/Test/tree|User:Jaime.Prilusky/Test/tree]]
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| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus alcalophilus subsp. halodurans boyer et al. 1973]] | + | [[Category: Alkalihalobacillus halodurans]] |
| - | [[Category: Ribonuclease H]] | + | [[Category: Large Structures]] |
| - | [[Category: Gan, J H]] | + | [[Category: Gan JH]] |
| - | [[Category: Gerlits, O]] | + | [[Category: Gerlits O]] |
| - | [[Category: Huang, Z]] | + | [[Category: Huang Z]] |
| - | [[Category: Jiang, J S]] | + | [[Category: Jiang JS]] |
| - | [[Category: Rob, A]] | + | [[Category: Rob A]] |
| - | [[Category: Endonuclease]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Hydrolase-rna-dna complex]]
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| - | [[Category: Magnesium]]
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| - | [[Category: Manganese]]
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| - | [[Category: Metal-binding]]
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| - | [[Category: Rnase h]]
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| - | [[Category: Selenium-dna/rna]]
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| - | [[Category: Selenium-modification]]
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