1ZET

X-ray data do not support hoogsteen base-pairing during replication by human polymerase iota


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 1T3N - determined by Nair, D.T., Johnson, R.E., Prakash, S., Prakash, L., Aggarwal, A.K.  

Literature

DNA polymerases: Hoogsteen base-pairing in DNA replication?

Wang, J.

(2005) Nature 437: E6-7; discussion E7

  • DOI: 10.1038/nature04199

  • PubMed Abstract: 
  • Human polymerase-iota belongs to the error-prone Y family of polymerases, which frequently incorporate incorrect nucleotides during DNA replication but can efficiently bypass DNA lesions. On the basis of X-ray diffraction data, Nair et al. propose th ...

    Human polymerase-iota belongs to the error-prone Y family of polymerases, which frequently incorporate incorrect nucleotides during DNA replication but can efficiently bypass DNA lesions. On the basis of X-ray diffraction data, Nair et al. propose that Hoogsteen base-pairing is adopted by DNA during its replication by this enzyme. Here I re-examine their X-ray data and find that the electron density is very weak for a Hoogsteen base pair formed between a template adenine deoxyribonucleotide in the syn conformation and a deoxythymidine 5'-triphosphate (dTTP), and that the fit is better for a normal Watson-Crick base pair. As a guanine-cytosine (G-C) base pair has no potential to form a Hoogsteen base pair at physiological pH, Hoogsteen base-pairing is unlikely to be used in replication by this polymerase.


    Related Citations: 
    • Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing.
      Nair, D.T.,Johnson, R.E.,Prakash, S.,Prakash, L.,Aggarwal, A.K.
      (2004) Nature 430: 377


    Organizational Affiliation

    Center for Structural Biology, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA wang@csb.yale.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polymerase (DNA directed) iota
A
388Homo sapiensMutation(s): 0 
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: 1
MoleculeChainsLengthOrganism
5'-D(P*AP*GP*GP*GP*(BRU)P*CP*CP*(BRU)P*(BRU)P*CP*CP*CP*CP*C)-3'T14N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*(DOC))-3'P13N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D 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
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
T
DNA LINKINGC9 H12 Br N2 O8 PDU
DOC
Query on DOC
P
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.261 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 98.831α = 90.00
b = 98.831β = 90.00
c = 202.755γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-04-19 
  • Released Date: 2005-07-19 
  • Deposition Author(s): Wang, J.

Revision History 

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-09-28
    Type: Other