PDBsum entry 4gp6

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protein ligands metals links
Transferase PDB id
Protein chains
171 a.a.
ADP ×2
_MG ×2
Waters ×237
PDB id:
Name: Transferase
Title: Polynucleotide kinase
Structure: Metallophosphoesterase. Chain: a, b. Engineered: yes
Source: Clostridium thermocellum. Organism_taxid: 203119. Strain: atcc 27405 / dsm 1237. Gene: cthe_2768. Expressed in: escherichia coli. Expression_system_taxid: 562
2.10Å     R-factor:   0.181     R-free:   0.228
Authors: L.K.Wang,U.Das,P.Smith,S.Shuman
Key ref: L.K.Wang et al. (2012). Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system. RNA, 18, 2277-2286. PubMed id: 23118415 DOI: 10.1261/rna.036061.112
20-Aug-12     Release date:   14-Nov-12    
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Protein chains
Pfam   ArchSchema ?
A3DJ38  (A3DJ38_CLOTH) -  Metallophosphoesterase
870 a.a.
171 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1261/rna.036061.112 RNA 18:2277-2286 (2012)
PubMed id: 23118415  
Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system.
L.K.Wang, U.Das, P.Smith, S.Shuman.
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. Here we report the crystal structure of the kinase domain of Clostridium thermocellum Pnkp bound to ATP•Mg(2+) (substrate complex) and ADP•Mg(2+) (product complex). The protein consists of a core P-loop phosphotransferase fold embellished by a distinctive homodimerization module composed of secondary structure elements derived from the N and C termini of the kinase domain. ATP is bound within a crescent-shaped groove formed by the P-loop ((15)GSSGSGKST(23)) and an overlying helix-loop-helix "lid." The α and β phosphates are engaged by a network of hydrogen bonds from Thr23 and the P-loop main-chain amides; the γ phosphate is anchored by the lid residues Arg120 and Arg123. The P-loop lysine (Lys21) and the catalytic Mg(2+) bridge the ATP β and γ phosphates. The P-loop serine (Ser22) is the sole enzymic constituent of the octahedral metal coordination complex. Structure-guided mutational analysis underscored the essential contributions of Lys21 and Ser22 in the ATP donor site and Asp38 and Arg41 in the phosphoacceptor site. Our studies suggest a catalytic mechanism whereby Asp38 (as general base) activates the polynucleotide 5'-OH for its nucleophilic attack on the γ phosphorus and Lys21 and Mg(2+) stabilize the transition state.