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1vgj

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[[Image:1vgj.gif|left|200px]]
 
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==Crystal structure of 2'-5' RNA ligase from Pyrococcus horikoshii==
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The line below this paragraph, containing "STRUCTURE_1vgj", creates the "Structure Box" on the page.
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<StructureSection load='1vgj' size='340' side='right'caption='[[1vgj]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.94&#8491;</td></tr>
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<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>
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{{STRUCTURE_1vgj| PDB=1vgj | SCENE= }}
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<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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/THPR_PYRHO THPR_PYRHO] Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester.[HAMAP-Rule:MF_01940]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vg/1vgj_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''Crystal structure of 2'-5' RNA ligase from Pyrococcus horikoshii'''
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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>
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==Overview==
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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.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1VGJ is a [[Single protein]] structure of sequence from [http://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].
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</div>
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<div class="pdbe-citations 1vgj" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/17142895 17142895]
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*[[RNA ligase|RNA ligase]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii]]
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[[Category: Single protein]]
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[[Category: Morita H]]
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[[Category: Morita, H.]]
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[[Category: Okada A]]
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[[Category: Okada, A.]]
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[[Category: Tanaka I]]
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[[Category: Tanaka, I.]]
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[[Category: Yao M]]
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[[Category: Yao, M.]]
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[[Category: Alpha+beta]]
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[[Category: Ligt-like]]
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[[Category: Structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 12:30:58 2008''
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Current revision

Crystal structure of 2'-5' RNA ligase from Pyrococcus horikoshii

PDB ID 1vgj

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