Crystal structure of DNA polymerase I from Thermus phage G20c

Ahlqvist, J.; Linares-Pastén, J.A.; Jasilionis, A.; Welin, M.; Håkansson, M.; Svensson, L.A.; Wang, L.; Watzlawick, H.; Ævarsson, A.; Friðjónsson, Ó.H.; Hreggviðsson, G.Ó.; Ketelsen Striberny, B.; Glomsaker, E.; Lanes, O.; Al-Karadaghi, S.; Nordberg Karlsson, E.

doi:10.1107/S2059798322009895

Figure 8
Palm domain with active-site residues of PolI_G20c compared with the Klenow fragment, DNA polymerase I from G. stearothermophilus and Taq polymerase. (a) Alignment of PolI_G20c with DNA polymerase I from G. stearothermophilus, E. coli DNA polymerase I and Taq polymerase generated in Jalview. Conserved residues (threshold 100%) are coloured according to ClustalX. The catalytic triad residues are marked with red boxes. α-Helices 18, 19, 20 and 21 of PolI_G20c, situated between the catalytic residue Asp481 and the two catalytic residues Asp683 and Glu684 in PolI_G20c, are predicted to make the same type of conformational shift, often described in the literature, as made by O-helices in the homologous polymerases. The substrate-coordinating residue Tyr549 is marked with a blue box and the whole palm domain that includes the finger and thumb subdomains as defined in InterPro is underlined with a black arrow. (b) Residues from the palm domain, chain A of BF (PDB entry 1knc, gold), the Klenow fragment (PDB entry 2kzz, orange) and Taq polymerase (PDB entry 5ytf, violet) are superposed and displayed on the palm domain of PolI_G20c chain A (ice blue). The catalytic amino-acid triad at the bottom of the cleft is displayed in ball-and-stick representation and is also enlarged, where Asp683, Glu684 and Asp481 in PolI_G20c are blue and the corresponding residues are violet in Taq polymerase, brown in DNA polymerase I from E. coli and dark gold in BF. (c) The catalytic residues of Taq polymerase (violet) are superimposed on the corresponding residues of PolI_G20c and the two Mg²⁺ ions from the Taq model (PDB entry 5ytf) are displayed in grey, along with the DNA substrate in light green, dGTP in dark green and Tyr671 in black, corresponding to Tyr549 in PolI_G20c, which is coloured according to standard atom colours. Part of the finger domain of Taq polymerase is also displayed in violet. The images were prepared with CCP4mg.

STRUCTURAL
BIOLOGY

ISSN: 2059-7983

Volume 78| Part 11| November 2022| Pages 1384-1398

https://doi.org/10.1107/S2059798322009895

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