3llm: Difference between revisions
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[[Image: | ==Crystal Structure Analysis of a RNA Helicase== | ||
<StructureSection load='3llm' size='340' side='right' caption='[[3llm]], [[Resolution|resolution]] 2.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3llm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LLM FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | |||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DDX9, DHX9, LKP, NDH2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3llm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3llm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3llm RCSB], [http://www.ebi.ac.uk/pdbsum/3llm PDBsum]</span></td></tr> | |||
</table> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ll/3llm_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
RNA helicases of the DExD/H-box superfamily are critically involved in all RNA-related processes. No crystal structures of human DExH-box domains had been determined previously, and their structures were difficult to predict owing to the low level of homology among DExH-motif-containing proteins from diverse species. Here we present the crystal structures of the conserved domain 1 of the DEIH-motif-containing helicase DHX9 and of the DEAD-box helicase DDX20. Both contain a RecA-like core, but DHX9 differs from DEAD-box proteins in the arrangement of secondary structural elements and is more similar to viral helicases such as NS3. The N-terminus of the DHX9 core contains two long alpha-helices that reside on the surface of the core without contributing to nucleotide binding. The RNA-polymerase-II-interacting minimal transactivation domain sequence forms an extended loop structure that resides in a hydrophobic groove on the surface of the DEIH domain. DHX9 lacks base-selective contacts and forms an unspecific but important stacking interaction with the base of the bound nucleotide, and our biochemical analysis confirms that the protein can hydrolyze ATP, guanosine 5'-triphosphate, cytidine 5'-triphosphate, and uridine 5'-triphosphate. Together, these findings allow the localization of functional motifs within the three-dimensional structure of a human DEIH helicase and show how these enzymes can bind nucleotide with high affinity in the absence of a Q-motif. | |||
Crystal structure of human RNA helicase A (DHX9): structural basis for unselective nucleotide base binding in a DEAD-box variant protein.,Schutz P, Wahlberg E, Karlberg T, Hammarstrom M, Collins R, Flores A, Schuler H J Mol Biol. 2010 Jul 23;400(4):768-82. Epub 2010 May 25. PMID:20510246<ref>PMID:20510246</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | ==See Also== | ||
*[[Helicase|Helicase]] | *[[Helicase|Helicase]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: Arrowsmith, C H | [[Category: Arrowsmith, C H]] | ||
[[Category: Berg, S Van Den | [[Category: Berg, S Van Den]] | ||
[[Category: Berglund, H | [[Category: Berglund, H]] | ||
[[Category: Bountra, C | [[Category: Bountra, C]] | ||
[[Category: Collins, R | [[Category: Collins, R]] | ||
[[Category: Flodin, S | [[Category: Flodin, S]] | ||
[[Category: Flores, A | [[Category: Flores, A]] | ||
[[Category: Graslund, S | [[Category: Graslund, S]] | ||
[[Category: Hammarstrom, M | [[Category: Hammarstrom, M]] | ||
[[Category: Johansson, A | [[Category: Johansson, A]] | ||
[[Category: Johansson, I | [[Category: Johansson, I]] | ||
[[Category: Kallas, A | [[Category: Kallas, A]] | ||
[[Category: Karlberg, T | [[Category: Karlberg, T]] | ||
[[Category: Kotenyova, T | [[Category: Kotenyova, T]] | ||
[[Category: Kotzsch, A | [[Category: Kotzsch, A]] | ||
[[Category: Kraulis, P | [[Category: Kraulis, P]] | ||
[[Category: Markova, N | [[Category: Markova, N]] | ||
[[Category: Moche, M | [[Category: Moche, M]] | ||
[[Category: Nielsen, T K | [[Category: Nielsen, T K]] | ||
[[Category: Nordlund, P | [[Category: Nordlund, P]] | ||
[[Category: Nyman, T | [[Category: Nyman, T]] | ||
[[Category: Persson, C | [[Category: Persson, C]] | ||
[[Category: Roos, A K | [[Category: Roos, A K]] | ||
[[Category: | [[Category: Structural genomic]] | ||
[[Category: Schuler, H M | [[Category: Schuler, H M]] | ||
[[Category: Schutz, P | [[Category: Schutz, P]] | ||
[[Category: Siponen, M I | [[Category: Siponen, M I]] | ||
[[Category: Svensson, L | [[Category: Svensson, L]] | ||
[[Category: Thorsell, A G | [[Category: Thorsell, A G]] | ||
[[Category: Tresaugues, L | [[Category: Tresaugues, L]] | ||
[[Category: Wahlberg, E | [[Category: Wahlberg, E]] | ||
[[Category: Weigelt, J | [[Category: Weigelt, J]] | ||
[[Category: Welin, M | [[Category: Welin, M]] | ||
[[Category: Wisniewska, M | [[Category: Wisniewska, M]] | ||
[[Category: Activator]] | [[Category: Activator]] | ||
[[Category: Alpha-beta-alpha]] | [[Category: Alpha-beta-alpha]] | ||
| Line 62: | Line 80: | ||
[[Category: Rna-binding]] | [[Category: Rna-binding]] | ||
[[Category: Sgc]] | [[Category: Sgc]] | ||