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2HVS

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

Summary for 2HVS
Entry DOI10.2210/pdb2hvs/pdb
Related2HVQ 2HVR
Descriptor5'-D(*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*TP*TP*G)-3', 5'-D(*CP*AP*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC)P*C)-3', 5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*T)-3', ... (7 entities in total)
Functional Keywordsrna, ligase, lysine adenylate, t4, protein dna-rna complex, ligase-dna-rna complex, ligase/dna/rna
Biological sourceEnterobacteria phage T4
Total number of polymer chains8
Total formula weight106199.70
Authors
Nandakumar, J.,Lima, C.D. (deposition date: 2006-07-30, release date: 2006-10-17, Last modification date: 2023-08-30)
Primary citationNandakumar, J.,Shuman, S.,Lima, C.D.
RNA Ligase Structures Reveal the Basis for RNA Specificity and Conformational Changes that Drive Ligation Forward.
Cell(Cambridge,Mass.), 127:71-84, 2006
Cited by
PubMed Abstract: 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.
PubMed: 17018278
DOI: 10.1016/j.cell.2006.08.038
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.5 Å)
Structure validation

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