1BNK

HUMAN 3-METHYLADENINE DNA GLYCOSYLASE COMPLEXED TO DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision.

Lau, A.Y.Scharer, O.D.Samson, L.Verdine, G.L.Ellenberger, T.

(1998) Cell 95: 249-258


  • PubMed Abstract: 
  • DNA N-glycosylases are base excision-repair proteins that locate and cleave damaged bases from DNA as the first step in restoring the genetic blueprint. The human enzyme 3-methyladenine DNA glycosylase removes a diverse group of damaged bases from DN ...

    DNA N-glycosylases are base excision-repair proteins that locate and cleave damaged bases from DNA as the first step in restoring the genetic blueprint. The human enzyme 3-methyladenine DNA glycosylase removes a diverse group of damaged bases from DNA, including cytotoxic and mutagenic alkylation adducts of purines. We report the crystal structure of human 3-methyladenine DNA glycosylase complexed to a mechanism-based pyrrolidine inhibitor. The enzyme has intercalated into the minor groove of DNA, causing the abasic pyrrolidine nucleotide to flip into the enzyme active site, where a bound water is poised for nucleophilic attack. The structure shows an elegant means of exposing a nucleotide for base excision as well as a network of residues that could catalyze the in-line displacement of a damaged base from the phosphodeoxyribose backbone.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (3-METHYLADENINE DNA GLYCOSYLASE)
A
216Homo sapiensGene Names: MPG (AAG, ANPG, MID1)
EC: 3.2.2.21
Find proteins for P29372 (Homo sapiens)
Go to Gene View: MPG
Go to UniProtKB:  P29372
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*CP*AP*TP*GP*YRRP*TP*TP*GP*CP*CP*T)-3')D13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3')E13N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YRR
Query on YRR
D
DNA LINKINGC5 H12 N O5 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.750α = 90.00
b = 57.100β = 90.00
c = 128.450γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHARPphasing
MLPHAREphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance