2hvs: Difference between revisions

Revision as of 06:46, 4 May 2008

Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 2'-deoxyribonucleotide at the nick

OverviewOverview

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 StructureAbout this Structure

2HVS is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.

ReferenceReference

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 Page seeded by OCA on Sun May 4 06:46:26 2008

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OCA

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 [[Image:2hvs.gif|left|200px]]
- {{Structure
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-|GENE= Y10A, 24.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])
+-->
-|DOMAIN=
+{{STRUCTURE_2hvs|  PDB=2hvs  |  SCENE=  }}
-|RELATEDENTRY=[[2hvq|2HVQ]], [[2hvr|2HVR]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvs OCA], [http://www.ebi.ac.uk/pdbsum/2hvs PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2hvs RCSB]</span>
-}}
 '''Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 2'-deoxyribonucleotide at the nick'''
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 [[Category: Lima, C D.]]
 [[Category: Nandakumar, J.]]
-[[Category: ligase]]
+[[Category: Ligase]]
-[[Category: lysine adenylate]]
+[[Category: Lysine adenylate]]
-[[Category: protein dna/rna complex]]
+[[Category: Protein dna/rna complex]]
-[[Category: rna]]
+[[Category: Rna]]
-[[Category: t4]]
+[[Category: T4]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 06:46:26 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:36:08 2008''