1MUD

CATALYTIC DOMAIN OF MUTY FROM ESCHERICHIA COLI, D138N MUTANT COMPLEXED TO ADENINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily.

Guan, Y.Manuel, R.C.Arvai, A.S.Parikh, S.S.Mol, C.D.Miller, J.H.Lloyd, S.Tainer, J.A.

(1998) Nat Struct Biol 5: 1058-1064

  • DOI: https://doi.org/10.1038/4168
  • Primary Citation of Related Structures:  
    1MUD, 1MUN, 1MUY

  • PubMed Abstract: 

    The DNA glycosylase MutY, which is a member of the Helix-hairpin-Helix (HhH) DNA glycosylase superfamily, excises adenine from mispairs with 8-oxoguanine and guanine. High-resolution crystal structures of the MutY catalytic core (cMutY), the complex with bound adenine, and designed mutants reveal the basis for adenine specificity and glycosyl bond cleavage chemistry. The two cMutY helical domains form a positively-charged groove with the adenine-specific pocket at their interface. The Watson-Crick hydrogen bond partners of the bound adenine are substituted by protein atoms, confirming a nucleotide flipping mechanism, and supporting a specific DNA binding orientation by MutY and structurally related DNA glycosylases.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenine DNA glycosylase225Escherichia coliMutation(s): 1 
Gene Names: mutYmicAb2961JW2928
EC: 3.2.2.31
UniProt
Find proteins for P17802 (Escherichia coli (strain K12))
Explore P17802 
Go to UniProtKB:  P17802
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17802
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
B [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ADE
Query on ADE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82α = 90
b = 49β = 122.6
c = 69.5γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 1.4: 2018-08-22
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations