4MDE

Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA

Summary for 4MDE

• Entry DOI: 10.2210/pdb4mde/pdb
• Related: 4GP6 4GP7 4JST 4JSY 4JT2 4JT4 4MDF
• Descriptor: Metallophosphoesterase, DNA (5'-D(P*CP*CP*TP*GP*T)-3'), GUANOSINE-5'-DIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: rna repair, p-loop phosphotransferase, transferase, hydrolase-dna complex, transferase-dna complex, transferase/dna
• Biological source: Clostridium thermocellum; More
• Total number of polymer chains: 4
• Total formula weight: 42851.66

Authors

Shuman, S.,Das, U.,Wang, L.K.,Smith, P.,Jacewicz, A. (deposition date: 2013-08-22, release date: 2013-11-06, Last modification date: 2024-02-28)

Primary citation

Das, U.,Wang, L.K.,Smith, P.,Jacewicz, A.,Shuman, S.
Structures of bacterial polynucleotide kinase in a Michaelis complex with GTP*Mg2+ and 5'-OH oligonucleotide and a product complex with GDP*Mg2+ and 5'-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition.
Nucleic Acids Res., 42:1152-1161, 2014

PubMed Abstract: Clostridium thermocellum polynucleotide kinase (CthPnk), the 5' end-healing module of a bacterial RNA repair system, catalyzes reversible phosphoryl transfer from an NTP donor to a 5'-OH polynucleotide acceptor. Here we report the crystal structures of CthPnk-D38N in a Michaelis complex with GTP•Mg(2+) and a 5'-OH oligonucleotide and a product complex with GDP•Mg(2+) and a 5'-PO4 oligonucleotide. The O5' nucleophile is situated 3.0 Å from the GTP γ phosphorus in the Michaelis complex, where it is coordinated by Asn38 and is apical to the bridging β phosphate oxygen of the GDP leaving group. In the product complex, the transferred phosphate has undergone stereochemical inversion and Asn38 coordinates the 5'-bridging phosphate oxygen of the oligonucleotide. The D38N enzyme is poised for catalysis, but cannot execute because it lacks Asp38-hereby implicated as the essential general base catalyst that abstracts a proton from the 5'-OH during the kinase reaction. Asp38 serves as a general acid catalyst during the 'reverse kinase' reaction by donating a proton to the O5' leaving group of the 5'-PO4 strand. The acceptor strand binding mode of CthPnk is distinct from that of bacteriophage T4 Pnk.

PubMed: 24150947
DOI: 10.1093/nar/gkt936

Experimental method

X-RAY DIFFRACTION (1.8 Å)