This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2c5u

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

T4 RNA Ligase (Rnl1) Crystal Structure

Structural highlights

2c5u is a 2 chain structure with sequence from Escherichia virus T4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.21Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1]

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^[2]

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

References

↑ Amitsur M, Levitz R, Kaufmann G. Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. EMBO J. 1987 Aug;6(8):2499-503. PMID:2444436
↑ 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 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==T4 RNA Ligase (Rnl1) Crystal Structure==
-<StructureSection load='2c5u' size='340' side='right' caption='[[2c5u]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
+<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/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>
+<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='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>
+</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='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='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='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'>[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>
-<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], [http://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]]
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Bpt4]]
+[[Category: Escherichia virus T4]]
-[[Category: Bird, L E]]
+[[Category: Large Structures]]
-[[Category: Bona, M K]]
+[[Category: Bird LE]]
-[[Category: Klarmann, G]]
+[[Category: Bona MK]]
-[[Category: LeGrice, S F.J]]
+[[Category: El Omari K]]
-[[Category: Omari, K El]]
+[[Category: Klarmann G]]
-[[Category: Ren, J]]
+[[Category: LeGrice SFJ]]
-[[Category: Stammers, D K]]
+[[Category: Ren J]]
-[[Category: Atp-binding]]
+[[Category: Stammers DK]]
-[[Category: Ligase]]
-[[Category: Nucleotidyl transferase]]
-[[Category: Rna ligase]]

2c5u

From Proteopedia

Current revision

T4 RNA Ligase (Rnl1) Crystal Structure

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox