4RNN

Crystal structure of human polymerase eta inserting dGMPnPP opposite DNA template containing an abasic site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.808 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite an Abasic Site by Human Translesion DNA Polymerase eta.

Patra, A.Zhang, Q.Lei, L.Su, Y.Egli, M.Guengerich, F.P.

(2015) J.Biol.Chem. 290: 8028-8038

  • DOI: 10.1074/jbc.M115.637561
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The most common lesion in DNA is an abasic site resulting from glycolytic cleavage of a base. In a number of cellular studies, abasic sites preferentially code for dATP insertion (the "A rule"). In some cases frameshifts are also common. X-ray struct ...

    The most common lesion in DNA is an abasic site resulting from glycolytic cleavage of a base. In a number of cellular studies, abasic sites preferentially code for dATP insertion (the "A rule"). In some cases frameshifts are also common. X-ray structures with abasic sites in oligonucleotides have been reported for several microbial and human DNA polymerases (pols), e.g. Dpo4, RB69, KlenTaq, yeast pol ι, human (h) pol ι, and human pol β. We reported previously that hpol η is a major pol involved in abasic site bypass (Choi, J.-Y., Lim, S., Kim, E. J., Jo, A., and Guengerich, F. P. (2010 J. Mol. Biol. 404, 34-44). hpol η inserted all four dNTPs in steady-state and pre-steady-state assays, preferentially inserting A and G. In LC-MS analysis of primer-template pairs, A and G were inserted but little C or T was inserted. Frameshifts were observed when an appropriate pyrimidine was positioned 5' to the abasic site in the template. In x-ray structures of hpol η with a non-hydrolyzable analog of dATP or dGTP opposite an abasic site, H-bonding was observed between the phosphate 5' to the abasic site and water H-bonded to N1 and N6 of A and N1 and O6 of G nucleoside triphosphate analogs, offering an explanation for what appears to be a "purine rule." A structure was also obtained for an A inserted and bonded in the primer opposite the abasic site, but it did not pair with a 5' T in the template. We conclude that hpol η, a major copying enzyme with abasic sites, follows a purine rule, which can also lead to frameshifts. The phenomenon can be explained with H-bonds.


    Organizational Affiliation

    From the Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146 f.guengerich@vanderbilt.edu.,From the Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146.,From the Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146 martin.egli@vanderbilt.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase eta
A
435Homo sapiensMutation(s): 0 
Gene Names: POLH (RAD30, RAD30A, XPV)
EC: 2.7.7.7
Find proteins for Q9Y253 (Homo sapiens)
Go to Gene View: POLH
Go to UniProtKB:  Q9Y253
Entity ID: 2
MoleculeChainsLengthOrganism
Nucleic acids Template: CAT(3DR)ATGACGCTT12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
Nucleic acids Primar: AGCGTCATP8synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
XG4
Query on XG4

Download SDF File 
Download CCD File 
A
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine
C10 H17 N6 O12 P3
DWGAAFQEGIMTIA-KVQBGUIXSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
T
DNA LINKINGC5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.808 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.168 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 98.556α = 90.00
b = 98.556β = 90.00
c = 81.880γ = 120.00
Software Package:
Software NamePurpose
MD2data collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-10-24 
  • Released Date: 2015-02-18 
  • Deposition Author(s): Patra, A., Egli, M.

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-04-22
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references