1MUN

CATALYTIC DOMAIN OF MUTY FROM ESCHERICHIA COLI D138N MUTANT

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.Mol.Biol. 5: 1058-1064

  • DOI: 10.1038/4168
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADENINE GLYCOSYLASE
A
225Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: mutY (micA)
EC: 3.2.2.31
Find proteins for P17802 (Escherichia coli (strain K12))
Go to UniProtKB:  P17802
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD
Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 82.500α = 90.00
b = 49.000β = 122.90
c = 69.400γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHELXL-97phasing
SHELXL-97model building
SHELXL-97refinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 1998-08-26 
  • Released Date: 1999-08-26 
  • Deposition Author(s): Guan, Y., Tainer, J.A.

Revision History 

  • Version 1.0: 1999-08-26
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance