5J2D

Ternary complex crystal structure of DNA polymerase Beta with C:C mismatch at the primer terminus

Summary for 5J2D

• Entry DOI: 10.2210/pdb5j2d/pdb
• Related: 5J0O 5J0P 5J0Q 5J0R 5J0S 5J0T 5J0U 5J0V 5J0W 5J0X 5J0Y 5J29 5J2A 5J2B 5J2C 5J2E 5J2F 5J2G 5J2H 5J2I 5J2J 5J2K
• Descriptor: DNA polymerase beta, Template Strand, Primer Strand, ... (9 entities in total)
• Functional Keywords: dna polymerase beta, mismatch extension, ternary complex, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (Human); More
• Cellular location: Nucleus: P06746
• Total number of polymer chains: 4
• Total formula weight: 48355.40

Authors

Batra, V.K.,Wilson, S.H. (deposition date: 2016-03-29, release date: 2016-10-26, Last modification date: 2023-09-27)

Primary citation

Batra, V.K.,Beard, W.A.,Pedersen, L.C.,Wilson, S.H.
Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism.
Structure, 24:1863-1875, 2016

PubMed Abstract: High-fidelity DNA synthesis requires that polymerases display a strong preference for right nucleotide insertion. When the wrong nucleotide is inserted, the polymerase deters extension from the mismatched DNA terminus. Twenty-three crystallographic structures of DNA polymerase β with terminal template-primer mismatches were determined as binary DNA and ternary pre-catalytic substrate complexes. These structures indicate that the mismatched termini adopt various distorted conformations that attempt to satisfy stacking and hydrogen-bonding interactions. The binary complex structures indicate an induced strain in the mismatched template nucleotide. Addition of a non-hydrolyzable incoming nucleotide stabilizes the templating nucleotide with concomitant strain in the primer terminus. Several dead-end ternary complex structures suggest that DNA synthesis might occur as the enzyme transitions from an open to a closed complex. The structures are consistent with an induced-fit mechanism where a mismatched terminus is misaligned relative to the correct incoming nucleotide to deter or delay further DNA synthesis.

PubMed: 27642161
DOI: 10.1016/j.str.2016.08.006

Experimental method

X-RAY DIFFRACTION (2.1 Å)