1vdx

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{{Seed}}
 
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[[Image:1vdx.png|left|200px]]
 
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==Crystal Structure of a Pyrococcus horikoshii protein with similarities to 2'5' RNA-ligase==
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The line below this paragraph, containing "STRUCTURE_1vdx", creates the "Structure Box" on the page.
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<StructureSection load='1vdx' size='340' side='right'caption='[[1vdx]], [[Resolution|resolution]] 2.40&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'>[[1vdx]] 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=1VDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VDX 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]] 2.4&#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=CL:CHLORIDE+ION'>CL</scene></td></tr>
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{{STRUCTURE_1vdx| PDB=1vdx | 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=1vdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vdx OCA], [https://pdbe.org/1vdx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vdx RCSB], [https://www.ebi.ac.uk/pdbsum/1vdx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vdx ProSAT], [https://www.topsan.org/Proteins/RSGI/1vdx TOPSAN]</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/vd/1vdx_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=1vdx 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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Cyclic phosphodiesterase and 2'-5' RNA ligase are members of a superfamily of proteins which share structural similarities even though their homology may be very low. A putative 2'-5' RNA ligase from Pyrococcus horikoshii has been crystallized and its X-ray crystallographic structure determined to 2.4 A. The protein crystallized in the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 44.07, b = 45.47, c = 93.17 A and one protein monomer in the asymmetric unit. The molecular-replacement probe was a 2'-5' RNA ligase from Thermus thermophilus which shares 30% sequence identity. The P. horikoshii RNA ligase has some structural features that have more in common with a cyclic phosphodiesterase from Arabidopsis thaliana with which it has no significant homology, yet an examination of the electrostatic surface potential clearly defines its relationship to the T. thermophilus RNA ligase. However, the size of the active-site cleft is smaller and less positively charged than that of the T. thermophilus homologue, suggesting that the actual substrate may be smaller than that previously postulated for the latter.
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===Crystal Structure of a Pyrococcus horikoshii protein with similarities to 2'5' RNA-ligase===
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Structure of a putative 2'-5' RNA ligase from Pyrococcus horikoshii.,Rehse PH, Tahirov TH Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1207-12. Epub 2005, Aug 16. PMID:16131753<ref>PMID:16131753</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1vdx" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_16131753}}, adds the Publication Abstract to the page
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*[[RNA ligase|RNA ligase]]
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(as it appears on PubMed at http://www.pubmed.gov), where 16131753 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16131753}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1VDX is a 1 chain 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=1VDX OCA].
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==Reference==
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Structure of a putative 2'-5' RNA ligase from Pyrococcus horikoshii., Rehse PH, Tahirov TH, Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1207-12. Epub 2005, Aug 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16131753 16131753]
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[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Rehse PH]]
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[[Category: Rehse, P H.]]
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[[Category: Tahirov TH]]
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[[Category: Tahirov, T H.]]
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[[Category: Ligase]]
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[[Category: National project on protein structural and functional analyse]]
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[[Category: Nppsfa]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: Rsgi]]
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[[Category: Structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 17:48:20 2008''
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Current revision

Crystal Structure of a Pyrococcus horikoshii protein with similarities to 2'5' RNA-ligase

PDB ID 1vdx

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