PDBsum entry 4qwc

Transferase/DNA

PDB id: 4qwc

Contents

Protein chains

342 a.a.

DNA/RNA

Ligands

ACT ×3

LTP ×2

Metals

_CA ×5

Waters ×175

References listed in PDB file

Key reference

• Title: Structural and kinetic insights into binding and incorporation of l-Nucleotide analogs by a y-Family DNA polymerase.
• Authors: V.Gaur, R.Vyas, J.D.Fowler, G.Efthimiopoulos, J.Y.Feng, Z.Suo.
• Ref.: Nucleic Acids Res, 2014, 42, 9984-9995. [DOI no: 10.1093/nar/gku709]
• PubMed id: 25104018

Abstract

Considering that all natural nucleotides (D-dNTPs) and the building blocks (D-dNMPs) of DNA chains possess D-stereochemistry, DNA polymerases and reverse transcriptases (RTs) likely possess strongD-stereoselectivity by preferably binding and incorporating D-dNTPs over unnatural L-dNTPs during DNA synthesis. Surprisingly, a structural basis for the discrimination against L-dNTPs by DNA polymerases or RTs has not been established although L-deoxycytidine analogs (lamivudine and emtricitabine) and L-thymidine (telbivudine) have been widely used as antiviral drugs for years. Here we report seven high-resolution ternary crystal structures of a prototype Y-family DNA polymerase, DNA, and D-dCTP, D-dCDP, L-dCDP, or the diphosphates and triphosphates of lamivudine and emtricitabine. These structures reveal that relative to D-dCTP, each of these L-nucleotides has its sugar ring rotated by 180° with an unusual O4'-endo sugar puckering and exhibits multiple triphosphate-binding conformations within the active site of the polymerase. Such rare binding modes significantly decrease the incorporation rates and efficiencies of these L-nucleotides catalyzed by the polymerase.