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6dod

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==Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 360 s at 21 C==
==Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 360 s at 21 C==
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<StructureSection load='6dod' size='340' side='right' caption='[[6dod]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
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<StructureSection load='6dod' size='340' side='right'caption='[[6dod]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6dod]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DOD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DOD FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6dod]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans_C-125 Alkalihalobacillus halodurans C-125] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DOD FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
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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]] 1.535&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></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=6dod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dod OCA], [http://pdbe.org/6dod PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dod RCSB], [http://www.ebi.ac.uk/pdbsum/6dod PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dod ProSAT]</span></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=6dod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dod OCA], [https://pdbe.org/6dod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dod RCSB], [https://www.ebi.ac.uk/pdbsum/6dod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dod ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
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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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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Catalysis by members of the RNase H superfamily of enzymes is generally believed to require only two Mg(2+) ions that are coordinated by active-site carboxylates. By examining the catalytic process of Bacillus halodurans RNase H1 in crystallo, however, we found that the two canonical Mg(2+) ions and an additional K(+) failed to align the nucleophilic water for RNA cleavage. Substrate alignment and product formation required a second K(+) and a third Mg(2+), which replaced the first K(+) and departed immediately after cleavage. A third transient Mg(2+) has also been observed for DNA synthesis, but in that case it coordinates the leaving group instead of the nucleophile as in the case of the RNase H1 hydrolysis reaction. These transient cations have no contact with the enzymes. Other DNA and RNA enzymes that catalyze consecutive cleavage and strand-transfer reactions in a single active site may similarly require cation trafficking coordinated by the substrate.
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Cation trafficking propels RNA hydrolysis.,Samara NL, Yang W Nat Struct Mol Biol. 2018 Aug;25(8):715-721. doi: 10.1038/s41594-018-0099-4. Epub, 2018 Aug 3. PMID:30076410<ref>PMID:30076410</ref>
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==See Also==
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6dod" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Ribonuclease H]]
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[[Category: Alkalihalobacillus halodurans C-125]]
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[[Category: Samara, N L]]
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[[Category: Large Structures]]
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[[Category: Yang, W]]
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[[Category: Synthetic construct]]
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[[Category: Divalent cation]]
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[[Category: Samara NL]]
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[[Category: Double helix]]
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[[Category: Yang W]]
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[[Category: Hydrolase]]
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[[Category: Hydrolase-dna-rna complex]]
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[[Category: In crystallo catalysis]]
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[[Category: Metal dependent catalysis]]
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[[Category: Monovalent cation]]
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[[Category: Protein-rna-dna complex]]
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[[Category: Rna hydrolysis]]
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Current revision

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 360 s at 21 C

PDB ID 6dod

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