4RU9

Crystal structure of human DNA polymerase eta inserting dCMPNPP opposite a MeFapy-dG adducted DNA template


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase eta and Sulfolobus solfataricus P2 Polymerase IV.

Patra, A.Banerjee, S.Johnson Salyard, T.L.Malik, C.K.Christov, P.P.Rizzo, C.J.Stone, M.P.Egli, M.

(2015) J.Am.Chem.Soc. 137: 7011-7014

  • DOI: 10.1021/jacs.5b02701
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N(6)-(2-Deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine (MeFapy-dG) arises from N7-methylation of deoxyguanosine followed by imidazole ring opening. The lesion has been reported to persist in animal tissues ...

    N(6)-(2-Deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine (MeFapy-dG) arises from N7-methylation of deoxyguanosine followed by imidazole ring opening. The lesion has been reported to persist in animal tissues. Previous in vitro replication bypass investigations of the MeFapy-dG adduct revealed predominant insertion of C opposite the lesion, dependent on the identity of the DNA polymerase (Pol) and the local sequence context. Here we report crystal structures of ternary Pol·DNA·dNTP complexes between MeFapy-dG-adducted DNA template:primer duplexes and the Y-family polymerases human Pol η and P2 Pol IV (Dpo4) from Sulfolobus solfataricus. The structures of the hPol η and Dpo4 complexes at the insertion and extension stages, respectively, are representative of error-free replication, with MeFapy-dG in the anti conformation and forming Watson-Crick pairs with dCTP or dC.


    Organizational Affiliation

    †Department of Biochemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,§Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Building 436E, Argonne, Illinois 60439, United States.,‡Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase eta
A
432Homo 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(MF7)ATGACGCTT12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
Nucleic acids Primar: AGCGTCATP8synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0KX
Query on 0KX

Download SDF File 
Download CCD File 
A
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine
C9 H17 N4 O12 P3
STYMTWKSQLVXJN-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  1 Unique
IDChainsTypeFormula2D DiagramParent
MF7
Query on MF7
T
DNA LINKINGC11 H18 N5 O8 P

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.159 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 98.971α = 90.00
b = 98.971β = 90.00
c = 81.624γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
PHASERphasing
MD2data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-11-18 
  • Released Date: 2015-08-05 
  • Deposition Author(s): Patra, A., Egli, M.

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release