1RRS | pdb_00001rrs

MutY adenine glycosylase in complex with DNA containing an abasic site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.275 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase

Fromme, J.C.Banerjee, A.Huang, S.J.Verdine, G.L.

(2004) Nature 427: 652-656

  • DOI: https://doi.org/10.1038/nature02306
  • Primary Citation Related Structures: 
    1RRQ, 1RRS, 1VRL

  • PubMed Abstract: 

    The genomes of aerobic organisms suffer chronic oxidation of guanine to the genotoxic product 8-oxoguanine (oxoG). Replicative DNA polymerases misread oxoG residues and insert adenine instead of cytosine opposite the oxidized base. Both bases in the resulting A*oxoG mispair are mutagenic lesions, and both must undergo base-specific replacement to restore the original C*G pair. Doing so represents a formidable challenge to the DNA repair machinery, because adenine makes up roughly 25% of the bases in most genomes. The evolutionarily conserved enzyme adenine DNA glycosylase (called MutY in bacteria and hMYH in humans) initiates repair of A*oxoG to C*G by removing the inappropriately paired adenine base from the DNA backbone. A central issue concerning MutY function is the mechanism by which A*oxoG mispairs are targeted among the vast excess of A*T pairs. Here we report the use of disulphide crosslinking to obtain high-resolution crystal structures of MutY-DNA lesion-recognition complexes. These structures reveal the basis for recognizing both lesions in the A*oxoG pair and for catalysing removal of the adenine base.


  • Organizational Affiliation
    • Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

Macromolecule Content 

  • Total Structure Weight: 49.12 kDa 
  • Atom Count: 3,113 
  • Modeled Residue Count: 366 
  • Deposited Residue Count: 391 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
MutYC [auth A]369Geobacillus stearothermophilusMutation(s): 0 
Gene Names: muty
EC: 3.2.2 (PDB Primary Data), 3.2.2.31 (UniProt)
UniProt
Find proteins for P83847 (Geobacillus stearothermophilus)
Explore P83847 
Go to UniProtKB:  P83847
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83847
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3'A [auth B]11N/A
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*TP*GP*TP*CP*CP*AP*(HPD)P*GP*TP*CP*T)-3'B [auth C]11N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.275 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.758α = 90
b = 85.539β = 90
c = 141.163γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description