3BJY

Catalytic core of Rev1 in complex with DNA (modified template guanine) and incoming nucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Protein-template-directed synthesis across an acrolein-derived DNA adduct by yeast Rev1 DNA polymerase

Nair, D.T.Johnson, R.E.Prakash, L.Prakash, S.Aggarwal, A.K.

(2008) Structure 16: 239-245

  • DOI: 10.1016/j.str.2007.12.009

  • PubMed Abstract: 
  • Acrolein is generated as the end product of lipid peroxidation and is also a ubiquitous environmental pollutant. Its reaction with the N2 of guanine leads to a cyclic gamma-HOPdG adduct that presents a block to normal replication. We show here that y ...

    Acrolein is generated as the end product of lipid peroxidation and is also a ubiquitous environmental pollutant. Its reaction with the N2 of guanine leads to a cyclic gamma-HOPdG adduct that presents a block to normal replication. We show here that yeast Rev1 incorporates the correct nucleotide C opposite a permanently ring-closed form of gamma-HOPdG (PdG) with nearly the same efficiency as opposite an undamaged G. The structural basis of this action lies in the eviction of the PdG adduct from the Rev1 active site, and the pairing of incoming dCTP with a "surrogate" arginine residue. We also show that yeast Polzeta can carry out the subsequent extension reaction. Together, our studies reveal how the exocyclic PdG adduct is accommodated in a DNA polymerase active site, and they show that the combined action of Rev1 and Polzeta provides for accurate and efficient synthesis through this potentially carcinogenic DNA lesion.


    Organizational Affiliation

    Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA repair protein REV1
A
434Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: REV1
EC: 2.7.7.-
Find proteins for P12689 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: REV1
Go to UniProtKB:  P12689
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DTP*DAP*DAP*(P)P*DGP*DTP*DAP*DGP*DGP*DGP*DGP*DAP*DGP*DGP*DAP*DT)-3')T16N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*DAP*DTP*DCP*DCP*DTP*DCP*DCP*DCP*DCP*DTP*DAP*(DOC))-3')P12N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCP
Query on DCP

Download SDF File 
Download CCD File 
A
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
DOC
Query on DOC
P
DNA LINKINGC9 H14 N3 O6 PDC
P
Query on P
T
DNA LINKINGC13 H18 N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.231 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 181.062α = 90.00
b = 199.578β = 90.00
c = 55.677γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
ADSCdata collection
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance