6X77

Rev1 R518A Ternary Complex with dCTP and Ca2+

Summary for 6X77

• Entry DOI: 10.2210/pdb6x77/pdb
• Descriptor: DNA (5'-D(P*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*G)-3'), DNA (5'-D(P*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3'), DNA repair protein REV1, ... (6 entities in total)
• Functional Keywords: dna polymerase, replication, replication-dna complex, replication/dna
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Total number of polymer chains: 3
• Total formula weight: 59384.73

Authors

Weaver, T.M.,Freudenthal, B.D. (deposition date: 2020-05-29, release date: 2020-09-30, Last modification date: 2023-10-18)

Primary citation

Weaver, T.M.,Cortez, L.M.,Khoang, T.H.,Washington, M.T.,Agarwal, P.K.,Freudenthal, B.D.
Visualizing Rev1 catalyze protein-template DNA synthesis.
Proc.Natl.Acad.Sci.USA, 117:25494-25504, 2020

PubMed Abstract: During DNA replication, replicative DNA polymerases may encounter DNA lesions, which can stall replication forks. One way to prevent replication fork stalling is through the recruitment of specialized translesion synthesis (TLS) polymerases that have evolved to incorporate nucleotides opposite DNA lesions. Rev1 is a specialized TLS polymerase that bypasses abasic sites, as well as minor-groove and exocyclic guanine adducts. Lesion bypass is accomplished using a unique protein-template mechanism in which the templating base is evicted from the DNA helix and the incoming dCTP hydrogen bonds with an arginine side chain of Rev1. To understand the protein-template mechanism at an atomic level, we employed a combination of time-lapse X-ray crystallography, molecular dynamics simulations, and DNA enzymology on the Rev1 protein. We find that Rev1 evicts the templating base from the DNA helix prior to binding the incoming nucleotide. Binding the incoming nucleotide changes the conformation of the DNA substrate to orient it for nucleotidyl transfer, although this is not coupled to large structural changes in Rev1 like those observed with other DNA polymerases. Moreover, we found that following nucleotide incorporation, Rev1 converts the pyrophosphate product to two monophosphates, which drives the reaction in the forward direction and prevents pyrophosphorolysis. Following nucleotide incorporation, the hydrogen bonds between the incorporated nucleotide and the arginine side chain are broken, but the templating base remains extrahelical. These postcatalytic changes prevent potentially mutagenic processive synthesis by Rev1 and facilitate dissociation of the DNA product from the enzyme.

PubMed: 32999062
DOI: 10.1073/pnas.2010484117

Experimental method

X-RAY DIFFRACTION (1.64 Å)