3B0Y

K263D mutant of PolX from Thermus thermophilus HB8 complexed with Ca-dGTP

Summary for 3B0Y

• Entry DOI: 10.2210/pdb3b0y/pdb
• Related: 3AU2 3B0X
• Descriptor: DNA polymerase beta family (X family), 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, ZINC ION, ... (6 entities in total)
• Functional Keywords: structural genomics, riken structural genomics/proteomics initiative, rsgi, polxc, php, dna polymerase, drp lyase, 3'-5' exonuclease, ap endonuclease, dna repair, nucleotide, dna, transferase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 1
• Total formula weight: 64958.74

Authors

Nakane, S.,Nakagawa, N.,Masui, R.,Kuramitsu, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2011-06-17, release date: 2012-05-02, Last modification date: 2023-11-01)

Primary citation

Nakane, S.,Ishikawa, H.,Nakagawa, N.,Kuramitsu, S.,Masui, R.
The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA.
J.Mol.Biol., 417:179-196, 2012

PubMed Abstract: DNA with single-nucleotide (1-nt) gaps can arise during various DNA processing events. These lesions are repaired by X-family DNA polymerases (PolXs) with high gap-filling activity. Some PolXs can bind productively to dNTPs in the absence of DNA and fill these 1-nt gaps. Although PolXs have a crucial role in efficient gap filling, currently, little is known of the kinetic and structural details of their productive dNTP binding. Here, we show that Thermus thermophilus HB8 PolX (ttPolX) had strong binding affinity for Mg(2+)-dNTPs in the absence of DNA and that it follows a Theorell-Chance (hit-and-run) mechanism with nucleotide binding first. Comparison of the intermediate crystal structures of ttPolX in a binary complex with dGTP and in a ternary complex with 1-nt gapped DNA and Mg(2+)-ddGTP revealed that the conformation of the incoming nucleotide depended on whether or not DNA was present. Furthermore, the Lys263 residue located between two guanosine conformations was essential to the strong binding affinity of the enzyme. The ability to bind to either syn-dNTP or anti-dNTP and the involvement of a Theorell-Chance mechanism are key aspects of the strong nucleotide-binding and efficient gap-filling activities of ttPolX.

PubMed: 22306405
DOI: 10.1016/j.jmb.2012.01.025

Experimental method

X-RAY DIFFRACTION (1.45 Å)