2hvs: Difference between revisions

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-[[Image:2hvs.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2hvs", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_2hvs|  PDB=2hvs  |  SCENE=  }}
-'''Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 2'-deoxyribonucleotide at the nick'''
+==Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 2'-deoxyribonucleotide at the nick==
+<StructureSection load='2hvs' size='340' side='right'caption='[[2hvs]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2hvs]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HVS 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]] 2.5&#8491;</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>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</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=2hvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvs OCA], [https://pdbe.org/2hvs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hvs RCSB], [https://www.ebi.ac.uk/pdbsum/2hvs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hvs ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RLIG2_BPT4 RLIG2_BPT4] Catalyzes intramolecular and intermolecular RNA strand joining (in vitro). May play a role in the repair of nicked RNA molecules.<ref>PMID:12228725</ref> <ref>PMID:17018278</ref>
+== 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/hv/2hvs_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=2hvs ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+T4 RNA ligase 2 (Rnl2) and kinetoplastid RNA editing ligases exemplify a family of RNA repair enzymes that seal 3'OH/5'PO(4) nicks in duplex RNAs via ligase adenylylation (step 1), AMP transfer to the nick 5'PO(4) (step 2), and attack by the nick 3'OH on the 5'-adenylylated strand to form a phosphodiester (step 3). Crystal structures are reported for Rnl2 at discrete steps along this pathway: the covalent Rnl2-AMP intermediate; Rnl2 bound to an adenylylated nicked duplex, captured immediately following step 2; and Rnl2 at an adenylylated nick in a state poised for step 3. These structures illuminate the stereochemistry of nucleotidyl transfer and reveal how remodeling of active-site contacts and conformational changes propel the ligation reaction forward. Mutational analysis and comparison of nick-bound structures of Rnl2 and human DNA ligase I highlight common and divergent themes of substrate recognition that can explain their specialization for RNA versus DNA repair.
-==Overview==
+RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward.,Nandakumar J, Shuman S, Lima CD Cell. 2006 Oct 6;127(1):71-84. PMID:17018278<ref>PMID:17018278</ref>
-T4 RNA ligase 2 (Rnl2) and kinetoplastid RNA editing ligases exemplify a family of RNA repair enzymes that seal 3'OH/5'PO(4) nicks in duplex RNAs via ligase adenylylation (step 1), AMP transfer to the nick 5'PO(4) (step 2), and attack by the nick 3'OH on the 5'-adenylylated strand to form a phosphodiester (step 3). Crystal structures are reported for Rnl2 at discrete steps along this pathway: the covalent Rnl2-AMP intermediate; Rnl2 bound to an adenylylated nicked duplex, captured immediately following step 2; and Rnl2 at an adenylylated nick in a state poised for step 3. These structures illuminate the stereochemistry of nucleotidyl transfer and reveal how remodeling of active-site contacts and conformational changes propel the ligation reaction forward. Mutational analysis and comparison of nick-bound structures of Rnl2 and human DNA ligase I highlight common and divergent themes of substrate recognition that can explain their specialization for RNA versus DNA repair.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-HVS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVS OCA].
+</div>
+<div class="pdbe-citations 2hvs" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward., Nandakumar J, Shuman S, Lima CD, Cell. 2006 Oct 6;127(1):71-84. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17018278 17018278]
+*[[RNA ligase|RNA ligase]]
-[[Category: Enterobacteria phage t4]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Lima, C D.]]
+__TOC__
-[[Category: Nandakumar, J.]]
+</StructureSection>
-[[Category: Ligase]]
+[[Category: Escherichia virus T4]]
-[[Category: Lysine adenylate]]
+[[Category: Large Structures]]
-[[Category: Protein dna/rna complex]]
+[[Category: Lima CD]]
-[[Category: Rna]]
+[[Category: Nandakumar J]]
-[[Category: T4]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 06:46:26 2008''