5TBC

PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTRATE, INCORPORATED (-)3TC-MP AND AN ANOTHER INCOMING (-)3TC-TP NUCLEOTIDE.

Summary for 5TBC

• Entry DOI: 10.2210/pdb5tbc/pdb
• Related: 5TB8 5TB9 5TBA 5TBB
• Descriptor: DNA polymerase beta, 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER, 10- MER PRIMER, ... (9 entities in total)
• Functional Keywords: x-family, pol beta, dna polymerase beta, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 49676.81

Authors

Vyas, R.,Suo, Z. (deposition date: 2016-09-11, release date: 2017-01-11, Last modification date: 2023-10-25)

Primary citation

Reed, A.J.,Vyas, R.,Raper, A.T.,Suo, Z.
Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase.
J. Am. Chem. Soc., 139:465-471, 2017

PubMed Abstract: DNA polymerases are essential enzymes that faithfully and efficiently replicate genomic information.1-3 The mechanism of nucleotide incorporation by DNA polymerases has been extensively studied structurally and kinetically, but several key steps following phosphodiester bond formation remain structurally uncharacterized due to utilization of natural nucleotides. It is thought that the release of pyrophosphate (PP) triggers reverse conformational changes in a polymerase in order to complete a full catalytic cycle as well as prepare for DNA translocation and subsequent incorporation events. Here, by using the triphosphates of chain-terminating antiviral drugs lamivudine ((-)3TC-TP) and emtricitabine ((-)FTC-TP), we structurally reveal the correct sequence of post-chemistry steps during nucleotide incorporation by human DNA polymerase β (hPolβ) and provide a structural basis for PP release. These post-catalytic structures reveal hPolβ in an open conformation with PP bound in the active site, thereby strongly suggesting that the reverse conformational changes occur prior to PP release. The results also help to refine the role of the newly discovered third divalent metal ion for DNA polymerase-catalyzed nucleotide incorporation. Furthermore, a post-chemistry structure of hPolβ in the open conformation, following incorporation of (-)3TC-MP, with a second (-)3TC-TP molecule bound to the active site in the absence of PP, suggests that nucleotide binding stimulates PP dissociation and occurs before polymerase translocation. Our structural characterization defines the order of the elusive post-chemistry steps in the canonical mechanism of a DNA polymerase.

PubMed: 27959534
DOI: 10.1021/jacs.6b11258

Experimental method

X-RAY DIFFRACTION (1.85 Å)