2c5u

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(Difference between revisions)

Revision as of 13:15, 10 September 2015

T4 RNA Ligase (Rnl1) Crystal Structure

Structural highlights

2c5u is a 2 chain structure with sequence from Bpt4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
NonStd Res:
Activity:	RNA ligase (ATP), with EC number 6.5.1.3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ El Omari K, Ren J, Bird LE, Bona MK, Klarmann G, LeGrice SF, Stammers DK. Molecular architecture and ligand recognition determinants for T4 RNA ligase. J Biol Chem. 2006 Jan 20;281(3):1573-9. Epub 2005 Nov 1. PMID:16263720 doi:10.1074/jbc.M509658200

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 2: / Line 2: @@
 <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 [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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C5U FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2c5u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C5U FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_ligase_(ATP) RNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.3 6.5.1.3] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c5u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c5u RCSB], [http://www.ebi.ac.uk/pdbsum/2c5u PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c5u OCA], [http://pdbe.org/2c5u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c5u RCSB], [http://www.ebi.ac.uk/pdbsum/2c5u PDBsum]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 26: / Line 26: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2c5u" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 33: / Line 34: @@
 __TOC__
 </StructureSection>
-[[Category: Enterobacteria phage t4]]
+[[Category: Bpt4]]
 [[Category: Bird, L E]]
 [[Category: Bona, M K]]

2c5u

From Proteopedia

Revision as of 13:15, 10 September 2015

T4 RNA Ligase (Rnl1) Crystal Structure

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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