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Wang, LK, Smith, P and Shuman, S (2013) Structure and mechanism of the 2',3' phosphatase component of the bacterial Pnkp-Hen1 RNA repair system. Nucleic Acids Res. 41:5864-73


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 PMC3675462 Online version:10.1093/nar/gkt221


Amino Acid Sequence; Bacterial Proteins/chemistry; Bacterial Proteins/genetics; Catalytic Domain; Clostridium thermocellum/enzymology; Methyltransferases/chemistry; Models, Molecular; Molecular Sequence Data; Mutation; Phosphoric Monoester Hydrolases/chemistry; Phosphoric Monoester Hydrolases/genetics; Polynucleotide 5'-Hydroxyl-Kinase/chemistry



Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status




Figure 2A tertiary structures as well as overlay shows conservation of structure to lambda phosphatase (with a citrase that mimics phosphate).

Missing: with/from
CACAO 11931


GO:0004721: phosphoprotein phosphatase activity



figure 2D shows aligned structures of the Cth and lambda phosphatase

Missing: with/from
CACAO 11959


See also


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