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1vgj
From Proteopedia
(Difference between revisions)
(New page: 200px<br /><applet load="1vgj" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vgj, resolution 1.94Å" /> '''Crystal structure of...) |
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| - | [[Image:1vgj.gif|left|200px]]<br /><applet load="1vgj" size="450" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="1vgj, resolution 1.94Å" /> | ||
| - | '''Crystal structure of 2'-5' RNA ligase from Pyrococcus horikoshii'''<br /> | ||
| - | == | + | ==Crystal structure of 2'-5' RNA ligase from Pyrococcus horikoshii== |
| - | Bacterial and archaeal 2'-5' RNA ligases, members of the 2H | + | <StructureSection load='1vgj' size='340' side='right'caption='[[1vgj]], [[Resolution|resolution]] 1.94Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[1vgj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VGJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VGJ 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]] 1.94Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1vgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vgj OCA], [https://pdbe.org/1vgj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vgj RCSB], [https://www.ebi.ac.uk/pdbsum/1vgj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vgj ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/THPR_PYRHO THPR_PYRHO] Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester.[HAMAP-Rule:MF_01940] | ||
| + | == 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/vg/1vgj_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/main_output.php?pdb_ID=1vgj ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Bacterial and archaeal 2'-5' RNA ligases, members of the 2H phosphoesterase superfamily, catalyze the linkage of the 5' and 3' exons via a 2'-5'-phosphodiester bond during tRNA-precursor splicing. The crystal structure of the 2'-5' RNA ligase PH0099 from Pyrococcus horikoshii OT3 was solved at 1.94 A resolution (PDB code 1vgj). The molecule has a bilobal alpha+beta arrangement with two antiparallel beta-sheets constituting a V-shaped active-site cleft, as found in other members of the 2H phosphoesterase superfamily. The present structure was significantly different from that determined previously at 2.4 A resolution (PDB code 1vdx) in the active-site cleft; the entrance to the cleft is wider and the active site is easily accessible to the substrate (RNA precursor) in our structure. Structural comparison with the 2'-5' RNA ligase from Thermus thermophilus HB8 also revealed differences in the RNA precursor-binding region. The structural differences in the active-site residues (tetrapeptide motifs H-X-T/S-X) between the members of the 2H phosphoesterase superfamily are discussed. | ||
| - | + | The structure of Pyrococcus horikoshii 2'-5' RNA ligase at 1.94 A resolution reveals a possible open form with a wider active-site cleft.,Gao YG, Yao M, Okada A, Tanaka I Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Dec 1;62(Pt, 12):1196-200. Epub 2006 Nov 30. PMID:17142895<ref>PMID:17142895</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 1vgj" style="background-color:#fffaf0;"></div> | |
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| - | + | ==See Also== | |
| + | *[[RNA ligase|RNA ligase]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Pyrococcus horikoshii]] | ||
| + | [[Category: Morita H]] | ||
| + | [[Category: Okada A]] | ||
| + | [[Category: Tanaka I]] | ||
| + | [[Category: Yao M]] | ||
Current revision
Crystal structure of 2'-5' RNA ligase from Pyrococcus horikoshii
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