6PZ3

Polymerase Eta-catalyzed insertion of correct G opposite template cytarabine (AraC) residue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.395 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into mutagenicity of anticancer nucleoside analog cytarabine during replication by DNA polymerase eta.

Rechkoblit, O.Johnson, R.E.Buku, A.Prakash, L.Prakash, S.Aggarwal, A.K.

(2019) Sci Rep 9: 16400-16400

  • DOI: 10.1038/s41598-019-52703-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cytarabine (AraC) is the mainstay chemotherapy for acute myeloid leukemia (AML). Whereas initial treatment with AraC is usually successful, most AML patients tend to relapse, and AraC treatment-induced mutagenesis may contribute to the development of ...

    Cytarabine (AraC) is the mainstay chemotherapy for acute myeloid leukemia (AML). Whereas initial treatment with AraC is usually successful, most AML patients tend to relapse, and AraC treatment-induced mutagenesis may contribute to the development of chemo-resistant leukemic clones. We show here that whereas the high-fidelity replicative polymerase Polδ is blocked in the replication of AraC, the lower-fidelity translesion DNA synthesis (TLS) polymerase Polη is proficient, inserting both correct and incorrect nucleotides opposite a template AraC base. Furthermore, we present high-resolution crystal structures of human Polη with a template AraC residue positioned opposite correct (G) and incorrect (A) incoming deoxynucleotides. We show that Polη can accommodate local perturbation caused by the AraC via specific hydrogen bonding and maintain a reaction-ready active site alignment for insertion of both correct and incorrect incoming nucleotides. Taken together, the structures provide a novel basis for the ability of Polη to promote AraC induced mutagenesis in relapsed AML patients.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77755-1061, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, Box 1677, 1425 Madison Avenue, New York, NY, 10029, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, Box 1677, 1425 Madison Avenue, New York, NY, 10029, USA. aneel.aggarwal@mssm.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase eta
A
435Homo sapiensMutation(s): 1 
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
DNA Primer strandP8synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA template containing cytarabine (AraC) residueT12synthetic 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

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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
CAR
Query on CAR
T
RNA LINKINGC9 H14 N3 O8 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.395 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 98.221α = 90.00
b = 98.221β = 90.00
c = 81.348γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA200575

Revision History 

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-12-04
    Type: Author supporting evidence