2VKC

Solution structure of the B3BP Smr domain


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 250 
  • Conformers Submitted: 28 
  • Selection Criteria: QUALITY 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution Structure and Characterization of the DNA- Binding Activity of the B3BP-Smr Domain.

Diercks, T.Ab, E.Daniels, M.A.De Jong, R.N.Besseling, R.Kaptein, R.Folkers, G.E.

(2008) J.Mol.Biol. 383: 1156

  • DOI: 10.1016/j.jmb.2008.09.005

  • PubMed Abstract: 
  • The MutS1 protein recognizes unpaired bases and initiates mismatch repair, which are essential for high-fidelity DNA replication. The homologous MutS2 protein does not contribute to mismatch repair, but suppresses homologous recombination. MutS2 lack ...

    The MutS1 protein recognizes unpaired bases and initiates mismatch repair, which are essential for high-fidelity DNA replication. The homologous MutS2 protein does not contribute to mismatch repair, but suppresses homologous recombination. MutS2 lacks the damage-recognition domain of MutS1, but contains an additional C-terminal extension: the small MutS-related (Smr) domain. This domain, which is present in both prokaryotes and eukaryotes, has previously been reported to bind to DNA and to possess nicking endonuclease activity. We determine here the solution structure of the functionally active Smr domain of the Bcl3-binding protein (also known as Nedd4-binding protein 2), a protein with unknown function that lacks other domains present in MutS proteins. The Smr domain adopts a two-layer alpha-beta sandwich fold, which has a structural similarity to the C-terminal domain of IF3, the R3H domain, and the N-terminal domain of DNase I. The most conserved residues are located in three loops that form a contiguous, exposed, and positively charged surface with distinct sequence identity for prokaryotic and eukaryotic Smr domains. NMR titration experiments and DNA binding studies using Bcl3-binding protein-Smr domain mutants suggested that these most conserved loop regions participate in DNA binding to single-stranded/double-stranded DNA junctions. Based on the observed DNA-binding-induced multimerization, the structural similarity with both subdomains of DNase I, and the experimentally identified DNA-binding surface, we propose a model for DNA recognition by the Smr domain.


    Organizational Affiliation

    Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Faculty of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEDD4-BINDING PROTEIN 2
A
135Homo sapiensMutation(s): 0 
Gene Names: N4BP2 (B3BP, KIAA1413)
EC: 3.-.-.-
Find proteins for Q86UW6 (Homo sapiens)
Go to Gene View: N4BP2
Go to UniProtKB:  Q86UW6
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 250 
  • Conformers Submitted: 28 
  • Selection Criteria: QUALITY 
  • Olderado: 2VKC Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance