4KHY

Ternary complex of rb69 mutant L415F with ribonucleotide at -3 position

Summary for 4KHY

• Entry DOI: 10.2210/pdb4khy/pdb
• Related: 4KHQ 4KHS 4KHU 4KHW 4KI4 4KI6
• Descriptor: DNA polymerase, DNA/RNA (5'-D(*AP*CP*AP*GP*G)-R(P*U)-D(P*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*C)-3'), ... (7 entities in total)
• Functional Keywords: ribonucleotide, transferase-dna complex, transferase/dna
• Biological source: Enterobacteria phage RB69
• Total number of polymer chains: 3
• Total formula weight: 115359.08

Authors

Clausen, A.R.,Pedersen, L.C. (deposition date: 2013-05-01, release date: 2013-10-09, Last modification date: 2023-09-20)

Primary citation

Clausen, A.R.,Murray, M.S.,Passer, A.R.,Pedersen, L.C.,Kunkel, T.A.
Structure-function analysis of ribonucleotide bypass by B family DNA replicases.
Proc.Natl.Acad.Sci.USA, 110:16802-16807, 2013

PubMed Abstract: Ribonucleotides are frequently incorporated into DNA during replication, they are normally removed, and failure to remove them results in replication stress. This stress correlates with DNA polymerase (Pol) stalling during bypass of ribonucleotides in DNA templates. Here we demonstrate that stalling by yeast replicative Pols δ and ε increases as the number of consecutive template ribonucleotides increases from one to four. The homologous bacteriophage RB69 Pol also stalls during ribonucleotide bypass, with a pattern most similar to that of Pol ε. Crystal structures of an exonuclease-deficient variant of RB69 Pol corresponding to multiple steps in single ribonucleotide bypass reveal that increased stalling is associated with displacement of Tyr391 and an unpreferred C2'-endo conformation for the ribose. Even less efficient bypass of two consecutive ribonucleotides in DNA correlates with similar movements of Tyr391 and displacement of one of the ribonucleotides along with the primer-strand DNA backbone. These structure-function studies have implications for cellular signaling by ribonucleotides, and they may be relevant to replication stress in cells defective in ribonucleotide excision repair, including humans suffering from autoimmune disease associated with RNase H2 defects.

PubMed: 24082122
DOI: 10.1073/pnas.1309119110

Experimental method

X-RAY DIFFRACTION (2.25 Å)