4J6O

Crystal Structure of the Phosphatase Domain of C. thermocellum (Bacterial) PnkP

Summary for 4J6O

• Entry DOI: 10.2210/pdb4j6o/pdb
• Related: 3TY5 3TY8 3TY9 4GP6 4GP7
• Descriptor: Metallophosphoesterase, CITRIC ACID, TRIETHYLENE GLYCOL, ... (7 entities in total)
• Functional Keywords: alpha/beta fold, calcineurin-like, phosphatase, metalloenzyme, hydrolase
• Biological source: Clostridium thermocellum
• Total number of polymer chains: 2
• Total formula weight: 61583.64

Authors

Wang, L.,Smith, P.,Shuman, S. (deposition date: 2013-02-11, release date: 2013-04-10, Last modification date: 2024-02-28)

Primary citation

Wang, L.K.,Smith, P.,Shuman, S.
Structure and mechanism of the 2',3' phosphatase component of the bacterial Pnkp-Hen1 RNA repair system.
Nucleic Acids Res., 41:5864-5873, 2013

PubMed Abstract: Pnkp is the end-healing and end-sealing component of an RNA repair system present in diverse bacteria from many phyla. Pnkp is composed of three catalytic modules: an N-terminal polynucleotide 5' kinase, a central 2',3' phosphatase and a C-terminal ligase. The phosphatase module is a Mn(2+)-dependent phosphodiesterase-monoesterase that dephosphorylates 2',3'-cyclic phosphate RNA ends. Here we report the crystal structure of the phosphatase domain of Clostridium thermocellum Pnkp with Mn(2+) and citrate in the active site. The protein consists of a core binuclear metallo-phosphoesterase fold (exemplified by bacteriophage λ phosphatase) embellished by distinctive secondary structure elements. The active site contains a single Mn(2+) in an octahedral coordination complex with Asp187, His189, Asp233, two citrate oxygens and a water. The citrate fills the binding site for the scissile phosphate, wherein it is coordinated by Arg237, Asn263 and His264. The citrate invades the site normally occupied by a second metal (engaged by Asp233, Asn263, His323 and His376), and thereby dislocates His376. A continuous tract of positive surface potential flanking the active site suggests an RNA binding site. The structure illuminates a large body of mutational data regarding the metal and substrate specificity of Clostridium thermocellum Pnkp phosphatase.

PubMed: 23595150
DOI: 10.1093/nar/gkt221

Experimental method

X-RAY DIFFRACTION (1.6 Å)