6X72

Rev1 Mg2+-facilitated Product Complex with two monophosphates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Visualizing Rev1 catalyze protein-template DNA synthesis.

Weaver, T.M.Cortez, L.M.Khoang, T.H.Washington, M.T.Agarwal, P.K.Freudenthal, B.D.

(2020) Proc Natl Acad Sci U S A 117: 25494-25504

  • DOI: 10.1002/em.22395
  • Primary Citation of Related Structures:  
    6X70, 6X72, 6X71, 6X74, 6X73, 6X76, 6X75, 6X77, 6X6Z

  • 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 ...

    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 Saccharomyces cerevisiae 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.


    Organizational Affiliation

    Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein REV1A442Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: REV1YOR346WO6339
EC: 2.7.7
Find proteins for P12689 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P12689 
Go to UniProtKB:  P12689
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*C*)-3')P13synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')T17synthetic construct
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PO4
      Query on PO4

      Download CCD File 
      A
      PHOSPHATE ION
      O4 P
      NBIIXXVUZAFLBC-UHFFFAOYSA-K
       Ligand Interaction
      GOL
      Query on GOL

      Download CCD File 
      A
      GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

      Download CCD File 
      A
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.19 Å
      • R-Value Free: 0.252 
      • R-Value Work: 0.186 
      • R-Value Observed: 0.192 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 62.408α = 90
      b = 73.814β = 90
      c = 117.147γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-3000data reduction
      HKL-3000data scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)--

      Revision History 

      • Version 1.0: 2020-09-30
        Type: Initial release
      • Version 1.1: 2020-10-21
        Changes: Database references