6NKY

Ternary complex crystal structure of K289M variant of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CHF analogue of dGTP

Summary for 6NKY

• Entry DOI: 10.2210/pdb6nky/pdb
• Descriptor: DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*TP*(2DT))-3'), DNA (5'-D(P*TP*TP*CP*GP*G)-3'), ... (9 entities in total)
• Functional Keywords: dna polymerase beta, conformational change, enzyme mechanism, lfer, transcription, transcription-dna complex, transcription/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 48373.73

Authors

Batra, V.K.,Wilson, S.H. (deposition date: 2019-01-07, release date: 2020-01-08, Last modification date: 2024-03-13)

Primary citation

Batra, V.K.,Alnajjar, K.S.,Sweasy, J.B.,McKenna, C.E.,Goodman, M.F.,Wilson, S.H.
Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Biochemistry, 59:955-963, 2020

PubMed Abstract: The human DNA polymerase (pol) β cancer variant K289M has altered polymerase activity , and the structure of wild-type pol β reveals that the K289 side chain contributes to a network of stabilizing interactions in a C-terminal region of the enzyme distal to the active site. Here, we probed the capacity of the K289M variant to tolerate strain introduced within the C-terminal region and active site. Strain was imposed by making use of a dGTP analogue containing a CF group substitution for the β-γ bridging oxygen atom. The ternary complex structure of the K289M variant displays an alteration in the C-terminal region, whereas the structure of wild-type pol β is not altered in the presence of the dGTP CF analogue. The alteration in the K289M variant impacts the active site, because the enzyme in the ternary complex fails to adopt the normal open to closed conformational change and assembly of the catalytically competent active site. These results reveal the importance of the K289-mediated stabilizing network in the C-terminal region of pol β and suggest an explanation for why the K289M cancer variant is deficient in polymerase activity even though the position 289 side chain is distal to the active site.

PubMed: 31999437
DOI: 10.1021/acs.biochem.9b01072

Experimental method

X-RAY DIFFRACTION (2.094 Å)