3I8D

The Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography

Summary for 3I8D

• Entry DOI: 10.2210/pdb3i8d/pdb
• Descriptor: Ribonuclease H, 5'-D(*CP*GP*CP*GP*AP*AP*TP*(DFT)P*CP*GP*CP*G)-3', GLYCEROL, ... (4 entities in total)
• Functional Keywords: rnase-h, rnase-h dna-complex, 2, 4-difluorotoluene, thymine isostere, hydrophobic base, endonuclease, hydrolase, magnesium, manganese, metal-binding, nuclease, hydrolase-dna complex, hydrolase/dna
• Biological source: Bacillus halodurans
• Cellular location: Cytoplasm : Q9KEI9
• Total number of polymer chains: 4
• Total formula weight: 38185.58

Authors

Egli, M.,Pallan, P.S. (deposition date: 2009-07-09, release date: 2009-09-01, Last modification date: 2023-09-06)

Primary citation

Pallan, P.S.,Egli, M.
Pairing geometry of the hydrophobic thymine analogue 2,4-difluorotoluene in duplex DNA as analyzed by X-ray crystallography.
J.Am.Chem.Soc., 131:12548-12549, 2009

PubMed Abstract: Certain DNA polymerases (pols) were found to efficiently insert A opposite the hydrophobic T isostere 2,4-difluorotoluene (F) and vice versa, resulting in the widely held belief that some pols rely on shape rather than H-bonding for accurate replication. Using X-ray crystallography we have analyzed the geometry of F:A pairs in duplex DNA and observed a distance between fluorine and the exocyclic amino group of A that is consistent with a H-bond, thus challenging the assumption that the F analogue is unable to engage in H-bonding as well as the steric hypothesis of DNA replication. Therefore, shape and H-bonding are inherently related, and steric constraints at a pol active site, or conferred by stacking or the DNA backbone conformation, may enable H-bonding by F.

PubMed: 19685868
DOI: 10.1021/ja905739j

Experimental method

X-RAY DIFFRACTION (1.61 Å)