View source for 3vn5


==Crystal structure of Aquifex aeolicus RNase H3==
<StructureSection load='3vn5' size='340' side='right'caption='[[3vn5]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3vn5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VN5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VN5 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98&#8491;</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=3vn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vn5 OCA], [https://pdbe.org/3vn5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vn5 RCSB], [https://www.ebi.ac.uk/pdbsum/3vn5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vn5 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RNH3_AQUAE RNH3_AQUAE] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
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== Publication Abstract from PubMed ==
The crystal structure of ribonuclease H3 from Aquifex aeolicus (Aae-RNase H3) was determined at 2.0 A resolution. Aae-RNase H3 consists of an N-terminal TATA box-binding protein (TBP)-like domain (N-domain) and a C-terminal RNase H domain (C-domain). The structure of the C-domain highly resembles that of Bacillus stearothermophilus RNase H3 (Bst-RNase H3), except that it contains three disulfide bonds, and the fourth conserved glutamate residue of the Asp-Glu-Asp-Glu active site motif (Glu198) is located far from the active site. These disulfide bonds were shown to contribute to hyper-stabilization of the protein. Non-conserved Glu194 was identified as the fourth active site residue. The structure of the N-domain without the C-domain also highly resembles that of Bst-RNase H3. However, the arrangement of the N-domain relative to the C-domain greatly varies for these proteins because of the difference in the linker size between the domains. The linker of Bst-RNase H3 is relatively long and flexible, while that of Aae-RNase H3 is short and assumes a helix formation. Biochemical characterizations of Aae-RNase H3 and its derivatives without the N- or C-domain or with a mutation in the N-domain indicate that the N-domain of Aae-RNase H3 is important for substrate binding, and uses the flat surface of the beta-sheet for substrate binding. However, this surface is located far from the active site and on the opposite side to the active site. We propose that the N-domain of Aae-RNase H3 is required for initial contact with the substrate. The resulting complex may be rearranged such that only the C-domain forms a complex with the substrate.

Structure and characterization of RNase H3 from Aquifex aeolicus.,Jongruja N, You DJ, Angkawidjaja C, Kanaya E, Koga Y, Kanaya S FEBS J. 2012 Aug;279(15):2737-53. doi: 10.1111/j.1742-4658.2012.08657.x. Epub, 2012 Jul 3. PMID:22686566<ref>PMID:22686566</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 3vn5" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Aquifex aeolicus VF5]]
[[Category: Large Structures]]
[[Category: Angkawidjaja C]]
[[Category: Eiko K]]
[[Category: Jongruja N]]
[[Category: Kanaya S]]
[[Category: Koga Y]]
[[Category: Takano K]]
[[Category: You DJ]]