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| | ==DEAD-box RNA helicase== | | ==DEAD-box RNA helicase== |
| - | <StructureSection load='5gju' size='340' side='right' caption='[[5gju]], [[Resolution|resolution]] 1.60Å' scene=''> | + | <StructureSection load='5gju' size='340' side='right'caption='[[5gju]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5gju]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GJU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5gju]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GJU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GJU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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]] 1.6Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">deaD, csdA, mssB, rhlD, b3162, JW5531 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=5gju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gju OCA], [https://pdbe.org/5gju PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gju RCSB], [https://www.ebi.ac.uk/pdbsum/5gju PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gju 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=5gju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gju OCA], [http://pdbe.org/5gju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gju RCSB], [http://www.ebi.ac.uk/pdbsum/5gju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gju ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DEAD_ECOLI DEAD_ECOLI]] DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation. Exhibits RNA-stimulated ATP hydrolysis and RNA unwinding activity at low temperature. Involved in 50S ribosomal subunit assembly, acting after SrmB, and could also play a role in the biogenesis of the 30S ribosomal subunit. In addition, is involved in mRNA decay, via formation of a cold-shock degradosome with RNase E. Also stimulates translation of some mRNAs, probably at the level of initiation.[HAMAP-Rule:MF_00964]<ref>PMID:10216955</ref> <ref>PMID:15148362</ref> <ref>PMID:15196029</ref> <ref>PMID:15554978</ref> <ref>PMID:17259309</ref> <ref>PMID:8552679</ref> | + | [https://www.uniprot.org/uniprot/DEAD_ECOLI DEAD_ECOLI] DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation. Exhibits RNA-stimulated ATP hydrolysis and RNA unwinding activity at low temperature. Involved in 50S ribosomal subunit assembly, acting after SrmB, and could also play a role in the biogenesis of the 30S ribosomal subunit. In addition, is involved in mRNA decay, via formation of a cold-shock degradosome with RNase E. Also stimulates translation of some mRNAs, probably at the level of initiation.[HAMAP-Rule:MF_00964]<ref>PMID:10216955</ref> <ref>PMID:15148362</ref> <ref>PMID:15196029</ref> <ref>PMID:15554978</ref> <ref>PMID:17259309</ref> <ref>PMID:8552679</ref> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | CsdA has been proposed to be essential for the biogenesis of ribosome and gene regulation after cold shock. However, the structure of CsdA and the function of its long C-terminal regions are still unclear. Here, we solved all of the domain structures of CsdA and found two previously uncharacterized auxiliary domains: a dimerization domain (DD) and an RNA-binding domain (RBD). Small-angle X-ray scattering experiments helped to track the conformational flexibilities of the helicase core domains and C-terminal regions. Biochemical assays revealed that DD is indispensable for stabilizing the CsdA dimeric structure. We also demonstrate for the first time that CsdA functions as a stable dimer at low temperature. The C-terminal regions are critical for RNA binding and efficient enzymatic activities. CsdA_RBD could specifically bind to the regions with a preference for single-stranded G-rich RNA, which may help to bring the helicase core to unwind the adjacent duplex. |
| | + | |
| | + | Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions.,Xu L, Wang L, Peng J, Li F, Wu L, Zhang B, Lv M, Zhang J, Gong Q, Zhang R, Zuo X, Zhang Z, Wu J, Tang Y, Shi Y Structure. 2017 Dec 5;25(12):1795-1808.e5. doi: 10.1016/j.str.2017.09.013. Epub, 2017 Oct 26. PMID:29107486<ref>PMID:29107486</ref> |
| | + | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 5gju" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Helicase 3D structures|Helicase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: RNA helicase]] | + | [[Category: Large Structures]] |
| - | [[Category: Li, F]] | + | [[Category: Li F]] |
| - | [[Category: Shi, Y]] | + | [[Category: Shi Y]] |
| - | [[Category: Wang, L]] | + | [[Category: Wang L]] |
| - | [[Category: Xu, L]] | + | [[Category: Xu L]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Reca-like]]
| + | |
| - | [[Category: Rna helicase]]
| + | |
| Structural highlights
Function
DEAD_ECOLI DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation. Exhibits RNA-stimulated ATP hydrolysis and RNA unwinding activity at low temperature. Involved in 50S ribosomal subunit assembly, acting after SrmB, and could also play a role in the biogenesis of the 30S ribosomal subunit. In addition, is involved in mRNA decay, via formation of a cold-shock degradosome with RNase E. Also stimulates translation of some mRNAs, probably at the level of initiation.[HAMAP-Rule:MF_00964][1] [2] [3] [4] [5] [6]
Publication Abstract from PubMed
CsdA has been proposed to be essential for the biogenesis of ribosome and gene regulation after cold shock. However, the structure of CsdA and the function of its long C-terminal regions are still unclear. Here, we solved all of the domain structures of CsdA and found two previously uncharacterized auxiliary domains: a dimerization domain (DD) and an RNA-binding domain (RBD). Small-angle X-ray scattering experiments helped to track the conformational flexibilities of the helicase core domains and C-terminal regions. Biochemical assays revealed that DD is indispensable for stabilizing the CsdA dimeric structure. We also demonstrate for the first time that CsdA functions as a stable dimer at low temperature. The C-terminal regions are critical for RNA binding and efficient enzymatic activities. CsdA_RBD could specifically bind to the regions with a preference for single-stranded G-rich RNA, which may help to bring the helicase core to unwind the adjacent duplex.
Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions.,Xu L, Wang L, Peng J, Li F, Wu L, Zhang B, Lv M, Zhang J, Gong Q, Zhang R, Zuo X, Zhang Z, Wu J, Tang Y, Shi Y Structure. 2017 Dec 5;25(12):1795-1808.e5. doi: 10.1016/j.str.2017.09.013. Epub, 2017 Oct 26. PMID:29107486[7]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Lu J, Aoki H, Ganoza MC. Molecular characterization of a prokaryotic translation factor homologous to the eukaryotic initiation factor eIF4A. Int J Biochem Cell Biol. 1999 Jan;31(1):215-29. PMID:10216955
- ↑ Charollais J, Dreyfus M, Iost I. CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit. Nucleic Acids Res. 2004 May 17;32(9):2751-9. Print 2004. PMID:15148362 doi:10.1093/nar/gkh603
- ↑ Bizebard T, Ferlenghi I, Iost I, Dreyfus M. Studies on three E. coli DEAD-box helicases point to an unwinding mechanism different from that of model DNA helicases. Biochemistry. 2004 Jun 22;43(24):7857-66. PMID:15196029 doi:10.1021/bi049852s
- ↑ Prud'homme-Genereux A, Beran RK, Iost I, Ramey CS, Mackie GA, Simons RW. Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold shock degradosome'. Mol Microbiol. 2004 Dec;54(5):1409-21. PMID:15554978 doi:http://dx.doi.org/10.1111/j.1365-2958.2004.04360.x
- ↑ Turner AM, Love CF, Alexander RW, Jones PG. Mutational analysis of the Escherichia coli DEAD box protein CsdA. J Bacteriol. 2007 Apr;189(7):2769-76. Epub 2007 Jan 26. PMID:17259309 doi:http://dx.doi.org/10.1128/JB.01509-06
- ↑ Jones PG, Mitta M, Kim Y, Jiang W, Inouye M. Cold shock induces a major ribosomal-associated protein that unwinds double-stranded RNA in Escherichia coli. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):76-80. PMID:8552679
- ↑ Xu L, Wang L, Peng J, Li F, Wu L, Zhang B, Lv M, Zhang J, Gong Q, Zhang R, Zuo X, Zhang Z, Wu J, Tang Y, Shi Y. Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions. Structure. 2017 Dec 5;25(12):1795-1808.e5. doi: 10.1016/j.str.2017.09.013. Epub, 2017 Oct 26. PMID:29107486 doi:http://dx.doi.org/10.1016/j.str.2017.09.013
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