2Q7F

Crystal structure of YrrB: a TPR protein with an unusual peptide-binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of YrrB: A TPR protein with an unusual peptide-binding site

Han, D.Oh, J.Kim, K.Lim, H.Kim, Y.

(2007) Biochem.Biophys.Res.Commun. 360: 784-790

  • DOI: 10.1016/j.bbrc.2007.06.129

  • PubMed Abstract: 
  • YrrB is a hypothetical protein containing a tetratricopeptide repeat (TPR) domain from a Gram-positive bacterium, Bacillus subtilis. We determined YrrB structure in the C2 space group to 2.5A resolution, which is the first TPR structure of the Gram-p ...

    YrrB is a hypothetical protein containing a tetratricopeptide repeat (TPR) domain from a Gram-positive bacterium, Bacillus subtilis. We determined YrrB structure in the C2 space group to 2.5A resolution, which is the first TPR structure of the Gram-positive bacterium B. subtilis. In contrast to other known TPR structures, the concave surface of the YrrB TPR domain is composed of the putative peptide-binding pocket lined with positively-charged residues. This unique charge distribution reveals that YrrB can interact with partner proteins via an unusual TPR-mediated interaction mode, compared to that of other TPR-containing structures. Functional annotation using genomics analysis suggested that YrrB may be an interacting mediator in the complex formation among RNA sulfuration components. No proteins containing a TPR domain have been identified in the biosynthesis of sulfur-containing biomolecules. Thus, YrrB could play a new role as a connecting module among those proteins in the conserved gene cluster for RNA sulfuration.


    Organizational Affiliation

    College of Medicine, Seoul National University, Yongon-Dong, Seoul 110-799, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YrrB protein
A, B
243Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: yrrB
Find proteins for O34452 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34452
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.938α = 90.00
b = 85.139β = 130.63
c = 69.048γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance