6VDD

POL domain of Pol1 from M. smegmatis complex with DNA primer-template and dNTP

Summary for 6VDD

• Entry DOI: 10.2210/pdb6vdd/pdb
• Descriptor: DNA polymerase I, DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A*(DCT))-3'), DNA (5'-D(P*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), ... (7 entities in total)
• Functional Keywords: mycobacteria, dna polymerase, apoenzyme, transferase-dna complex, transferase/dna
• Biological source: Mycolicibacterium smegmatis; More
• Total number of polymer chains: 6
• Total formula weight: 149923.69

Authors

Shuman, S.,Goldgur, Y.,Ghosh, S. (deposition date: 2019-12-24, release date: 2020-02-12, Last modification date: 2024-03-06)

Primary citation

Ghosh, S.,Goldgur, Y.,Shuman, S.
Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme.
Nucleic Acids Res., 48:3165-3180, 2020

PubMed Abstract: Mycobacterial Pol1 is a bifunctional enzyme composed of an N-terminal DNA flap endonuclease/5' exonuclease domain (FEN/EXO) and a C-terminal DNA polymerase domain (POL). Here we document additional functions of Pol1: FEN activity on the flap RNA strand of an RNA:DNA hybrid and reverse transcriptase activity on a DNA-primed RNA template. We report crystal structures of the POL domain, as apoenzyme and as ternary complex with 3'-dideoxy-terminated DNA primer-template and dNTP. The thumb, palm, and fingers subdomains of POL form an extensive interface with the primer-template and the triphosphate of the incoming dNTP. Progression from an open conformation of the apoenzyme to a nearly closed conformation of the ternary complex entails a disordered-to-ordered transition of several segments of the thumb and fingers modules and an inward motion of the fingers subdomain-especially the O helix-to engage the primer-template and dNTP triphosphate. Distinctive structural features of mycobacterial Pol1 POL include a manganese binding site in the vestigial 3' exonuclease subdomain and a non-catalytic water-bridged magnesium complex at the protein-DNA interface. We report a crystal structure of the bifunctional FEN/EXO-POL apoenzyme that reveals the positions of two active site metals in the FEN/EXO domain.

PubMed: 32034423
DOI: 10.1093/nar/gkaa075

Experimental method

X-RAY DIFFRACTION (1.9 Å)