3RWU

RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Difluorotoluene Nucleoside

Summary for 3RWU

• Entry DOI: 10.2210/pdb3rwu/pdb
• Descriptor: DNA polymerase, 5'-D(*TP*CP*GP*(DFT)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3', 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3', ... (6 entities in total)
• Functional Keywords: difluorotoluene, datp, y567a, y567a mutant, transferase-dna complex, transferase/dna
• Biological source: Enterobacteria phage RB69; More
• Total number of polymer chains: 3
• Total formula weight: 114454.45

Authors

Xia, S.,Konigsberg, W.H.,Wang, J. (deposition date: 2011-05-09, release date: 2011-06-29, Last modification date: 2024-02-28)

Primary citation

Xia, S.,Konigsberg, W.H.,Wang, J.
Hydrogen-Bonding Capability of a Templating Difluorotoluene Nucleotide Residue in an RB69 DNA Polymerase Ternary Complex.
J.Am.Chem.Soc., 133:10003-10005, 2011

PubMed Abstract: Results obtained using 2,4-difluorotoluene nucleobase (dF) as a nonpolar thymine isostere by Kool and colleagues challenged the Watson-Crick dogma that hydrogen bonds between complementary bases are an absolute requirement for accurate DNA replication. Here, we report crystal structure of an RB69 DNA polymerase L561A/S565G/Y567A triple mutant ternary complex with a templating dF opposite dTTP at 1.8 Å-resolution. In this structure, direct hydrogen bonds were observed between: (i) dF and the incoming dTTP, (ii) dF and residue G568 of the polymerase, and (iii) dF and ordered water molecules surrounding the nascent base pair. Therefore, this structure provides evidence that a templating dF can form novel hydrogen bonds with the incoming dTTP and with the enzyme that differ from those formed with a templating dT.

PubMed: 21667997
DOI: 10.1021/ja2021735

Experimental method

X-RAY DIFFRACTION (2.33 Å)