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6dok

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Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 25 mM K+ for 120 s at 21 C (dataset 1)

Structural highlights

6dok is a 4 chain structure with sequence from Alkalihalobacillus halodurans and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.38Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNH1_HALH5 Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.^[1]

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Nowotny M, Gaidamakov SA, Crouch RJ, Yang W. Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell. 2005 Jul 1;121(7):1005-16. PMID:15989951 doi:http://dx.doi.org/10.1016/j.cell.2005.04.024
↑ Samara NL, Yang W. Cation trafficking propels RNA hydrolysis. Nat Struct Mol Biol. 2018 Aug;25(8):715-721. doi: 10.1038/s41594-018-0099-4. Epub, 2018 Aug 3. PMID:30076410 doi:http://dx.doi.org/10.1038/s41594-018-0099-4

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6dok"

Categories: Alkalihalobacillus halodurans | Large Structures | Synthetic construct | Samara NL | Yang W

@@ Line 3: / Line 3: @@
 <StructureSection load='6dok' size='340' side='right'caption='[[6dok]], [[Resolution|resolution]] 1.38&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6dok]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DOK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6DOK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6dok]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans Alkalihalobacillus halodurans] 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=6DOK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DOK FirstGlance]. <br>
-</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.38&#8491;</td></tr>
-<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>
+<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'>[http://proteopedia.org/fgij/fg.htm?mol=6dok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dok OCA], [http://pdbe.org/6dok PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dok RCSB], [http://www.ebi.ac.uk/pdbsum/6dok PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dok ProSAT]</span></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=6dok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dok OCA], [https://pdbe.org/6dok PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dok RCSB], [https://www.ebi.ac.uk/pdbsum/6dok PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dok ProSAT]</span></td></tr>
 </table>
 == 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;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 26: @@
 __TOC__
 </StructureSection>
+[[Category: Alkalihalobacillus halodurans]]
 [[Category: Large Structures]]
-[[Category: Ribonuclease H]]
+[[Category: Synthetic construct]]
-[[Category: Samara, N L]]
+[[Category: Samara NL]]
-[[Category: Yang, W]]
+[[Category: Yang W]]
-[[Category: Divalent cation]]
-[[Category: Double helix]]
-[[Category: Hydrolase-dna-rna complex]]
-[[Category: In crystallo catalysis]]
-[[Category: Metal dependent catalysis]]
-[[Category: Monovalent cation]]
-[[Category: Protein-rna-dna complex]]
-[[Category: Rna hydrolysis]]

6dok

From Proteopedia

Current revision

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 25 mM K+ for 120 s at 21 C (dataset 1)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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