3TY5

Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP

Summary for 3TY5

• Entry DOI: 10.2210/pdb3ty5/pdb
• Descriptor: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase, ADENOSINE-5'-TRIPHOSPHATE, ADENOSINE-5'-DIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: dna ligase/mrna capping enzyme, rna ligase, adenylyltransferase, hen1, transferase
• Biological source: Clostridium thermocellum
• Total number of polymer chains: 2
• Total formula weight: 96035.08

Authors

Smith, P.,Wang, L.,Shuman, S. (deposition date: 2011-09-23, release date: 2012-01-25, Last modification date: 2024-02-28)

Primary citation

Smith, P.,Wang, L.K.,Nair, P.A.,Shuman, S.
The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family.
Proc.Natl.Acad.Sci.USA, 109:2296-2301, 2012

PubMed Abstract: Pnkp is the end-healing and end-sealing component of an RNA repair system present in diverse bacteria from ten different phyla. To gain insight to the mechanism and evolution of this repair system, we determined the crystal structures of the ligase domain of Clostridium thermocellum Pnkp in three functional states along the reaction pathway: apoenzyme, ligase • ATP substrate complex, and covalent ligase-AMP intermediate. The tertiary structure is composed of a classical ligase nucleotidyltransferase module that is embellished by a unique α-helical insert module and a unique C-terminal α-helical module. Structure-guided mutational analysis identified active site residues essential for ligase adenylylation. Pnkp defines a new RNA ligase family with signature structural and functional properties.

PubMed: 22308407
DOI: 10.1073/pnas.1116827109

Experimental method

X-RAY DIFFRACTION (2.4 Å)