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 

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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
  • Primary Citation of Related Structures:  
    3BJY

  • 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 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 ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein REV1A434Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: REV1
EC: 2.7.7
UniProt
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

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*DTP*DAP*DAP*(P)P*DGP*DTP*DAP*DGP*DGP*DGP*DGP*DAP*DGP*DGP*DAP*DT)-3')B [auth T]16N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*DAP*DTP*DCP*DCP*DTP*DCP*DCP*DCP*DCP*DTP*DAP*(DOC))-3')C [auth P]12N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCP (Subject of Investigation/LOI)
Query on DCP

Download Ideal Coordinates CCD File 
D [auth A]2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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
b = 199.578β = 90
c = 55.677γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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