5TZV

Binary complex crystal structure of DNA Polymerase Beta with G:T mismatch at the primer terminus

Replaces:  5J0V

Summary for 5TZV

• Entry DOI: 10.2210/pdb5tzv/pdb
• Descriptor: DNA polymerase beta, DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*T)-3'), ... (6 entities in total)
• Functional Keywords: dna polymerase, fidelity, mismatch extension, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (Human); More
• Cellular location: Nucleus: P06746
• Total number of polymer chains: 4
• Total formula weight: 47798.84

Authors

Wilson, S.H.,Batra, V.K. (deposition date: 2016-11-22, release date: 2016-12-07, Last modification date: 2023-10-04)

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 Å)