1NKU | pdb_00001nku

NMR Solution Structure of Zinc-binding protein 3-methyladenine DNA glycosylase I (TAG)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 25 
  • Selection Criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 1NKU

This is version 1.4 of the entry. See complete history

Literature

A Novel Zinc Snap Motif Conveys Structural Stability to 3-Methyladenine DNA Glycosylase I

Kwon, K.Cao, C.Stivers, J.T.

(2003) J Biological Chem 278: 19442-19446

  • DOI: https://doi.org/10.1074/jbc.M300934200
  • Primary Citation Related Structures: 
    1NKU

  • PubMed Abstract: 

    The Escherichia coli 3-methyladenine DNA glycosylase I (TAG) is a DNA repair enzyme that excises 3-methyladenine in DNA and is the smallest member of the helix-hairpin-helix (HhH) superfamily of DNA glycosylases. Despite many studies over the last 25 years, there has been no suggestion that TAG was a metalloprotein. However, here we establish by heteronuclear NMR and other spectroscopic methods that TAG binds 1 eq of Zn2+ extremely tightly. A family of refined NMR structures shows that 4 conserved residues contributed from the amino- and carboxyl-terminal regions of TAG (Cys4, His17, His175, and Cys179) form a Zn2+ binding site. The Zn2+ ion serves to tether the otherwise unstructured amino- and carboxyl-terminal regions of TAG. We propose that this unexpected "zinc snap" motif in the TAG family (CX(12-17)HX(approximately 150)HX(3)C) serves to stabilize the HhH domain thereby mimicking the functional role of protein-protein interactions in larger HhH superfamily members.


  • Organizational Affiliation
    • Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185, USA.

Macromolecule Content 

  • Total Structure Weight: 21.2 kDa 
  • Atom Count: 1,481 
  • Modeled Residue Count: 187 
  • Deposited Residue Count: 187 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3-Methyladenine Dna Glycosylase I (TAG)187Escherichia coliMutation(s): 0 
EC: 3.2.2.20
UniProt
Find proteins for P05100 (Escherichia coli (strain K12))
Explore P05100 
Go to UniProtKB:  P05100
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05100
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 25 
  • Selection Criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-03
    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: 2022-02-23
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection