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4gp6, resolution 2.10Å ()
Ligands: ,
Gene: Cthe_2768 (Clostridium thermocellum ATCC 27405)
Activity: Polynucleotide 5'-hydroxyl-kinase, with EC number
Related: 4gp7, 3ty5, 3ty8, 3ty9, 4drf, 4e6n

Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml

Polynucleotide kinase

Publication Abstract from PubMed

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 alpha and beta phosphates are engaged by a network of hydrogen bonds from Thr23 and the P-loop main-chain amides; the gamma phosphate is anchored by the lid residues Arg120 and Arg123. The P-loop lysine (Lys21) and the catalytic Mg(2+) bridge the ATP beta and gamma 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 gamma phosphorus and Lys21 and Mg(2+) stabilize the transition state.

Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system., Wang LK, Das U, Smith P, Shuman S, RNA. 2012 Nov 1. PMID:23118415

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

4gp6 is a 2 chain structure with sequence from Clostridium thermocellum atcc 27405. Full crystallographic information is available from OCA.

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