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PDBsum entry 4khq

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Transferase/DNA PDB id
4khq
Jmol
Contents
Protein chain
899 a.a.
DNA/RNA
Ligands
DUP
Metals
_NA ×8
_CA ×3
Waters ×578

References listed in PDB file
Key reference
Title Structure-Function analysis of ribonucleotide bypass by b family DNA replicases.
Authors A.R.Clausen, M.S.Murray, A.R.Passer, L.C.Pedersen, T.A.Kunkel.
Ref. Proc Natl Acad Sci U S A, 2013, 110, 16802-16807. [DOI no: 10.1073/pnas.1309119110]
PubMed id 24082122
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.
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