5ULX

Structure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine crystallized in the presence of dCTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-iota.

Jain, R.Choudhury, J.R.Buku, A.Johnson, R.E.Prakash, L.Prakash, S.Aggarwal, A.K.

(2017) Sci Rep 7: 43904-43904

  • DOI: 10.1038/srep43904
  • Primary Citation of Related Structures:  5ULW

  • PubMed Abstract: 
  • N1-methyl-deoxyadenosine (1-MeA) is formed by methylation of deoxyadenosine at the N1 atom. 1-MeA presents a block to replicative DNA polymerases due to its inability to participate in Watson-Crick (W-C) base pairing. Here we determine how human DNA ...

    N1-methyl-deoxyadenosine (1-MeA) is formed by methylation of deoxyadenosine at the N1 atom. 1-MeA presents a block to replicative DNA polymerases due to its inability to participate in Watson-Crick (W-C) base pairing. Here we determine how human DNA polymerase-ι (Polι) promotes error-free replication across 1-MeA. Steady state kinetic analyses indicate that Polι is ~100 fold more efficient in incorporating the correct nucleotide T versus the incorrect nucleotide C opposite 1-MeA. To understand the basis of this selectivity, we determined ternary structures of Polι bound to template 1-MeA and incoming dTTP or dCTP. In both structures, template 1-MeA rotates to the syn conformation but pairs differently with dTTP versus dCTP. Thus, whereas dTTP partakes in stable Hoogsteen base pairing with 1-MeA, dCTP fails to gain a "foothold" and is largely disordered. Together, our kinetic and structural studies show how Polι maintains discrimination between correct and incorrect incoming nucleotide opposite 1-MeA in preserving genome integrity.


    Organizational Affiliation

    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase iota
A
420Homo sapiensGene Names: POLI (RAD30B)
EC: 2.7.7.7
Find proteins for Q9UNA4 (Homo sapiens)
Go to Gene View: POLI
Go to UniProtKB:  Q9UNA4
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3')P7unidentified
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*(MA7)P*GP*GP*GP*TP*CP*CP*T)-3')T11unidentified
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MA7
Query on MA7
T
DNA LINKINGC11 H17 N5 O6 PDA
DOC
Query on DOC
P
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.216 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 97.915α = 90.00
b = 97.915β = 90.00
c = 202.239γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of Environmental Health SciencesUnited StatesR01-ES021452

Revision History 

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence