3GYH

Crystal Structure Analysis of S. Pombe ATL in complex with damaged DNA containing POB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Flipping of alkylated DNA damage bridges base and nucleotide excision repair.

Tubbs, J.L.Latypov, V.Kanugula, S.Butt, A.Melikishvili, M.Kraehenbuehl, R.Fleck, O.Marriott, A.Watson, A.J.Verbeek, B.McGown, G.Thorncroft, M.Santibanez-Koref, M.F.Millington, C.Arvai, A.S.Kroeger, M.D.Peterson, L.A.Williams, D.M.Fried, M.G.Margison, G.P.Pegg, A.E.Tainer, J.A.

(2009) Nature 459: 808-813

  • DOI: 10.1038/nature08076
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Alkyltransferase-like proteins (ATLs) share functional motifs with the cancer chemotherapy target O(6)-alkylguanine-DNA alkyltransferase (AGT) and paradoxically protect cells from the biological effects of DNA alkylation damage, despite lacking the r ...

    Alkyltransferase-like proteins (ATLs) share functional motifs with the cancer chemotherapy target O(6)-alkylguanine-DNA alkyltransferase (AGT) and paradoxically protect cells from the biological effects of DNA alkylation damage, despite lacking the reactive cysteine and alkyltransferase activity of AGT. Here we determine Schizosaccharomyces pombe ATL structures without and with damaged DNA containing the endogenous lesion O(6)-methylguanine or cigarette-smoke-derived O(6)-4-(3-pyridyl)-4-oxobutylguanine. These results reveal non-enzymatic DNA nucleotide flipping plus increased DNA distortion and binding pocket size compared to AGT. Our analysis of lesion-binding site conservation identifies new ATLs in sea anemone and ancestral archaea, indicating that ATL interactions are ancestral to present-day repair pathways in all domains of life. Genetic connections to mammalian XPG (also known as ERCC5) and ERCC1 in S. pombe homologues Rad13 and Swi10 and biochemical interactions with Escherichia coli UvrA and UvrC combined with structural results reveal that ATLs sculpt alkylated DNA to create a genetic and structural intersection of base damage processing with nucleotide excision repair.


    Organizational Affiliation

    Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alkyltransferase-like protein 1
X
116Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: atl1
Find proteins for Q9UTN9 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9UTN9
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*CP*AP*TP*GP*GP*CP*TP*AP*GP*TP*A)-3')Y13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*G)-3')Z13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PBO
Query on PBO

Download SDF File 
Download CCD File 
Y
1-PYRIDIN-3-YLBUTAN-1-ONE
C9 H11 N O
JORUAYHMUWRFNM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.240 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 60.180α = 90.00
b = 60.180β = 90.00
c = 235.546γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance