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| | ==Structure of the second domain (residues 207-368) of the Bacillus subtilis YxiN protein== | | ==Structure of the second domain (residues 207-368) of the Bacillus subtilis YxiN protein== |
| - | <StructureSection load='2hjv' size='340' side='right' caption='[[2hjv]], [[Resolution|resolution]] 1.95Å' scene=''> | + | <StructureSection load='2hjv' size='340' side='right'caption='[[2hjv]], [[Resolution|resolution]] 1.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2hjv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HJV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HJV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2hjv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HJV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HJV FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2g0c|2g0c]]</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]] 1.95Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dbpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=2hjv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hjv OCA], [https://pdbe.org/2hjv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hjv RCSB], [https://www.ebi.ac.uk/pdbsum/2hjv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hjv ProSAT]</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=2hjv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hjv OCA], [http://pdbe.org/2hjv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hjv RCSB], [http://www.ebi.ac.uk/pdbsum/2hjv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hjv ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DBPA_BACSU DBPA_BACSU]] DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit. Has an RNA-dependent ATPase activity, which is specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses the energy of ATP hydrolysis to destabilize and unwind short rRNA duplexes (Probable).<ref>PMID:10481020</ref> <ref>PMID:19474341</ref> | + | [https://www.uniprot.org/uniprot/DBPA_BACSU DBPA_BACSU] DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit. Has an RNA-dependent ATPase activity, which is specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses the energy of ATP hydrolysis to destabilize and unwind short rRNA duplexes (Probable).<ref>PMID:10481020</ref> <ref>PMID:19474341</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Helicase|Helicase]] | + | *[[Helicase 3D structures|Helicase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Vibrio subtilis ehrenberg 1835]] | + | [[Category: Bacillus subtilis]] |
| - | [[Category: Caruthers, J M]] | + | [[Category: Large Structures]] |
| - | [[Category: McKay, D B]] | + | [[Category: Caruthers JM]] |
| - | [[Category: Hydrolase]] | + | [[Category: McKay DB]] |
| - | [[Category: Parallel alpha-beta]]
| + | |
| Structural highlights
Function
DBPA_BACSU DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit. Has an RNA-dependent ATPase activity, which is specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses the energy of ATP hydrolysis to destabilize and unwind short rRNA duplexes (Probable).[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The Bacillus subtilis RNA helicase YxiN is a modular three-domain protein. The first two domains form a conserved helicase core that couples an ATPase activity to an RNA duplex-destabilization activity, while the third domain recognizes a stem-loop of 23S ribosomal RNA with high affinity and specificity. The structure of the second domain, amino-acid residues 207-368, has been solved to 1.95 A resolution, revealing a parallel alphabeta-fold. The crystallographic asymmetric unit contains two protomers; superposition shows that they differ substantially in two segments of peptide that overlap the conserved helicase sequence motifs V and VI, while the remainder of the domain is isostructural. The conformational variability of these segments suggests that induced fit is intrinsic to the recognition of ligands (ATP and RNA) and the coupling of the ATPase activity to conformational changes.
Structure of the second domain of the Bacillus subtilis DEAD-box RNA helicase YxiN.,Caruthers JM, Hu Y, McKay DB Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Dec 1;62(Pt, 12):1191-5. Epub 2006 Nov 30. PMID:17142894[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kossen K, Uhlenbeck OC. Cloning and biochemical characterization of Bacillus subtilis YxiN, a DEAD protein specifically activated by 23S rRNA: delineation of a novel sub-family of bacterial DEAD proteins. Nucleic Acids Res. 1999 Oct 1;27(19):3811-20. PMID:10481020
- ↑ Karow AR, Klostermeier D. A conformational change in the helicase core is necessary but not sufficient for RNA unwinding by the DEAD box helicase YxiN. Nucleic Acids Res. 2009 Jul;37(13):4464-71. doi: 10.1093/nar/gkp397. Epub 2009, May 27. PMID:19474341 doi:http://dx.doi.org/10.1093/nar/gkp397
- ↑ Caruthers JM, Hu Y, McKay DB. Structure of the second domain of the Bacillus subtilis DEAD-box RNA helicase YxiN. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Dec 1;62(Pt, 12):1191-5. Epub 2006 Nov 30. PMID:17142894 doi:10.1107/S1744309106044642
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