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

Experimental Data Snapshot

  • Resolution: 2.49 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.211 

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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: https://doi.org/10.1016/j.bbrc.2007.06.129
  • Primary Citation of Related Structures:  

  • 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-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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YrrB protein
A, B
243Bacillus subtilisMutation(s): 0 
Gene Names: yrrB
Find proteins for O34452 (Bacillus subtilis (strain 168))
Explore O34452 
Go to UniProtKB:  O34452
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34452
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.49 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.938α = 90
b = 85.139β = 130.63
c = 69.048γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Refinement description