3vn5: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[ | ==Crystal structure of Aquifex aeolicus RNase H3== | ||
<StructureSection load='3vn5' size='340' side='right' caption='[[3vn5]], [[Resolution|resolution]] 1.98Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3vn5]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VN5 FirstGlance]. <br> | |||
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aq_1768, rnhC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 Aquifex aeolicus VF5])</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='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=3vn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vn5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vn5 RCSB], [http://www.ebi.ac.uk/pdbsum/3vn5 PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | |||
*[[Ribonuclease|Ribonuclease]] | |||
== | *[[User:Jaime.Prilusky/Test/tree|User:Jaime.Prilusky/Test/tree]] | ||
[[ | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Aquifex aeolicus vf5]] | [[Category: Aquifex aeolicus vf5]] | ||
[[Category: Ribonuclease H]] | [[Category: Ribonuclease H]] | ||
[[Category: Angkawidjaja, C | [[Category: Angkawidjaja, C]] | ||
[[Category: Eiko, K | [[Category: Eiko, K]] | ||
[[Category: Jongruja, N | [[Category: Jongruja, N]] | ||
[[Category: Kanaya, S | [[Category: Kanaya, S]] | ||
[[Category: Koga, Y | [[Category: Koga, Y]] | ||
[[Category: Takano, K | [[Category: Takano, K]] | ||
[[Category: You, D J | [[Category: You, D J]] | ||
[[Category: Hydrolase]] | [[Category: Hydrolase]] | ||
[[Category: Rnase h3]] | [[Category: Rnase h3]] | ||
Revision as of 20:46, 9 December 2014
Crystal structure of Aquifex aeolicus RNase H3Crystal structure of Aquifex aeolicus RNase H3
Structural highlights
Publication Abstract from PubMedThe 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||