2c5u

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:48, 23 October 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2c5u.png|left|200px]]
 
-
{{STRUCTURE_2c5u| PDB=2c5u | SCENE= }}
+
==T4 RNA Ligase (Rnl1) Crystal Structure==
 +
<StructureSection load='2c5u' size='340' side='right'caption='[[2c5u]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
 +
== Structural highlights ==
 +
<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>
 +
</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>
 +
<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>
 +
<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>
 +
</table>
 +
== Function ==
 +
[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>
 +
== 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/c5/2c5u_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2c5u ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
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.
-
===T4 RNA Ligase (Rnl1) Crystal Structure===
+
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>
-
{{ABSTRACT_PUBMED_16263720}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 2c5u" style="background-color:#fffaf0;"></div>
-
[[2c5u]] is a 2 chain structure of [[RNA ligase]] 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].
+
==See Also==
==See Also==
*[[RNA ligase|RNA ligase]]
*[[RNA ligase|RNA ligase]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:016263720</ref><references group="xtra"/>
+
__TOC__
-
[[Category: Enterobacteria phage t4]]
+
</StructureSection>
-
[[Category: Bird, L E.]]
+
[[Category: Escherichia virus T4]]
-
[[Category: Bona, M K.]]
+
[[Category: Large Structures]]
-
[[Category: Klarmann, G.]]
+
[[Category: Bird LE]]
-
[[Category: Legrice, S F.J.]]
+
[[Category: Bona MK]]
-
[[Category: Omari, K El.]]
+
[[Category: El Omari K]]
-
[[Category: Ren, J.]]
+
[[Category: Klarmann G]]
-
[[Category: Stammers, D K.]]
+
[[Category: LeGrice SFJ]]
-
[[Category: Atp-binding]]
+
[[Category: Ren J]]
-
[[Category: Ligase]]
+
[[Category: Stammers DK]]
-
[[Category: Nucleotidyl transferase]]
+
-
[[Category: Rna ligase]]
+

Current revision

T4 RNA Ligase (Rnl1) Crystal Structure

PDB ID 2c5u

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2c5u"
Personal tools