3G6Y

Ternary complex of DNA Polymerase iota:DNA:dTTP with an abasic site at the templating position


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.220 

wwPDB Validation  3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

DNA Synthesis across an Abasic Lesion by Human DNA Polymerase iota

Nair, D.T.Johnson, R.E.Prakash, L.Prakash, S.Aggarwal, A.K.

(2009) Structure 17: 530-537

  • DOI: 10.1016/j.str.2009.02.015
  • Primary Citation of Related Structures:  3G6V, 3G6X

  • PubMed Abstract: 
  • Abasic sites are among the most abundant DNA lesions formed in human cells, and they present a strong block to replication. DNA polymerase iota (Poliota) is one of the few DNA Pols that does not follow the A-rule opposite an abasic site. We present h ...

    Abasic sites are among the most abundant DNA lesions formed in human cells, and they present a strong block to replication. DNA polymerase iota (Poliota) is one of the few DNA Pols that does not follow the A-rule opposite an abasic site. We present here three structures of human Poliota in complex with DNAs containing an abasic lesion and dGTP, dTTP, or dATP as the incoming nucleotide. The structures reveal a mechanism of translesion synthesis across an abasic lesion that differs from that in other Pols. Both the abasic lesion and the incoming dNTPs are intrahelical and are closely apposed across a constricted active site cleft. The dNTPs partake in distinct networks of hydrogen bonds in the "void" opposite the lesion. These different patterns of hydrogen bonds, as well as stacking interactions, may underlie Poliota's small preference for insertion of dGTP over other nucleotides opposite this common lesion.


    Organizational Affiliation

    Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
Molecule Chains Sequence Length Organism Details
DNA polymerase iota
A
420 Homo sapiens Gene 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: 2
Molecule Chains Length Organism
Primer DNA strand P 7 N/A
Entity ID: 3
Molecule Chains Length Organism
Template DNA strand T 11 N/A
Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TTP
Query on TTP

Download SDF File 
Download CCD File 
A
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
ID Chains Type Formula 2D Diagram Parent
3DR
Query on 3DR
T
DNA LINKING C5 H11 O6 P

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DOC
Query on DOC
P
DNA LINKING C9 H14 N3 O6 P DC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.220 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å) Angle (°)
a = 98.114 α = 90.00
b = 98.114 β = 90.00
c = 202.823 γ = 120.00
Software Package:
Software Name Purpose
HKL-2000 data reduction
JDirector data collection
CNS refinement
REFMAC refinement
HKL-2000 data scaling
AMoRE phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description