3GVA

Crystal Structure Analysis of S. Pombe ATL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.221 

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:  
    3GVA, 3GX4, 3GYH

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alkyltransferase-like protein 1AB116Schizosaccharomyces pombeMutation(s): 0 
Gene Names: atl1SPAC1250.04c
Find proteins for Q9UTN9 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9UTN9 
Go to UniProtKB:  Q9UTN9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.221 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.298α = 90
b = 46.298β = 90
c = 169.277γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance