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==Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 10 mM Mg2+ and 75 mM K+ for 40 s at 21 C== | ==Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 10 mM Mg2+ and 75 mM K+ for 40 s at 21 C== | ||
<StructureSection load='6dp3' size='340' side='right' caption='[[6dp3]], [[Resolution|resolution]] 1.46Å' scene=''> | <StructureSection load='6dp3' size='340' side='right'caption='[[6dp3]], [[Resolution|resolution]] 1.46Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6dp3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DP3 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6dp3]] 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=6DP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DP3 FirstGlance]. <br> | ||
</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 | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.461Å</td></tr> | ||
<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></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6dp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dp3 OCA], [https://pdbe.org/6dp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dp3 RCSB], [https://www.ebi.ac.uk/pdbsum/6dp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dp3 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [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;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6dp3" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Alkalihalobacillus halodurans C-125]] | ||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Samara NL]] | |||
[[Category: | [[Category: Yang W]] | ||
[[Category: | |||
[[Category: | |||
[[Category: | |||
Latest revision as of 09:11, 11 October 2023
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 10 mM Mg2+ and 75 mM K+ for 40 s at 21 CCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 10 mM Mg2+ and 75 mM K+ for 40 s at 21 C
Structural highlights
FunctionRNH1_HALH5 Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.[1] Publication Abstract from PubMedCatalysis 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. 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[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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