2c5u

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[[Image:2c5u.png|left|200px]]
 
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{{STRUCTURE_2c5u| PDB=2c5u | SCENE= }}
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==T4 RNA Ligase (Rnl1) Crystal Structure==
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<StructureSection load='2c5u' size='340' side='right'caption='[[2c5u]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2c5u]] is a 2 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=2C5U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C5U FirstGlance]. <br>
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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]] 2.21&#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=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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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=2c5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c5u OCA], [https://pdbe.org/2c5u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c5u RCSB], [https://www.ebi.ac.uk/pdbsum/2c5u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c5u ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RLIG_BPT4 RLIG_BPT4] Involved in countering a host defense mechanism which activates T4-induced anticodon nuclease and shuts off viral translation. Repairs 5'-PO4 and 3'-OH groups in tRNA(Lys).<ref>PMID:2444436</ref>
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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/c5/2c5u_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2c5u 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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RNA ligase type 1 from bacteriophage T4 (Rnl1) is involved in countering a host defense mechanism by repairing 5'-PO4 and 3'-OH groups in tRNA(Lys). Rnl1 is widely used as a reagent in molecular biology. Although many structures for DNA ligases are available, only fragments of RNA ligases such as Rnl2 are known. We report the first crystal structure of a complete RNA ligase, Rnl1, in complex with adenosine 5'-(alpha,beta-methylenetriphosphate) (AMPcPP). The N-terminal domain is related to the equivalent region of DNA ligases and Rnl2 and binds AMPcPP but with further interactions from the additional N-terminal 70 amino acids in Rnl1 (via Tyr37 and Arg54) and the C-terminal domain (Gly269 and Asp272). The active site contains two metal ions, consistent with the two-magnesium ion catalytic mechanism. The C-terminal domain represents a new all alpha-helical fold and has a charge distribution and architecture for helix-nucleic acid groove interaction compatible with tRNA binding.
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===T4 RNA Ligase (Rnl1) Crystal Structure===
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Molecular architecture and ligand recognition determinants for T4 RNA ligase.,El Omari K, Ren J, Bird LE, Bona MK, Klarmann G, LeGrice SF, Stammers DK J Biol Chem. 2006 Jan 20;281(3):1573-9. Epub 2005 Nov 1. PMID:16263720<ref>PMID:16263720</ref>
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{{ABSTRACT_PUBMED_16263720}}
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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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==About this Structure==
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<div class="pdbe-citations 2c5u" style="background-color:#fffaf0;"></div>
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[[2c5u]] is a 2 chain structure with 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=2C5U OCA].
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==See Also==
==See Also==
*[[RNA ligase|RNA ligase]]
*[[RNA ligase|RNA ligase]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:016263720</ref><references group="xtra"/>
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__TOC__
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[[Category: Enterobacteria phage t4]]
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</StructureSection>
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[[Category: Bird, L E.]]
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[[Category: Escherichia virus T4]]
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[[Category: Bona, M K.]]
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[[Category: Large Structures]]
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[[Category: Klarmann, G.]]
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[[Category: Bird LE]]
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[[Category: Legrice, S F.J.]]
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[[Category: Bona MK]]
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[[Category: Omari, K El.]]
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[[Category: El Omari K]]
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[[Category: Ren, J.]]
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[[Category: Klarmann G]]
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[[Category: Stammers, D K.]]
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[[Category: LeGrice SFJ]]
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[[Category: Atp-binding]]
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[[Category: Ren J]]
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[[Category: Ligase]]
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[[Category: Stammers DK]]
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[[Category: Nucleotidyl transferase]]
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[[Category: Rna ligase]]
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Current revision

T4 RNA Ligase (Rnl1) Crystal Structure

PDB ID 2c5u

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