Crystal structure of an uncommon cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases

Experimental Data Snapshot

  • Resolution: 1.38 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Crystal Structure of an Uncommon Cellulosome-Related Protein Module from Ruminococcus flavefaciens That Resembles Papain-Like Cysteine Peptidases.

Levy-Assaraf, M.Voronov-Goldman, M.Rozman Grinberg, I.Weiserman, G.Shimon, L.J.Jindou, S.Borovok, I.White, B.A.Bayer, E.A.Lamed, R.Frolow, F.

(2013) PLoS One 8: e56138-e56138

  • DOI: https://doi.org/10.1371/journal.pone.0056138
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Ruminococcus flavefaciens is one of the predominant fiber-degrading bacteria found in the rumen of herbivores. Bioinformatic analysis of the recently sequenced genome indicated that this bacterium produces one of the most intricate cellulosome systems known to date. A distinct ORF, encoding for a multi-modular protein, RflaF_05439, was discovered during mining of the genome sequence. It is composed of two tandem modules of currently undefined function that share 45% identity and a C-terminal X-dockerin modular dyad. Gaining insight into the diversity, architecture and organization of different types of proteins in the cellulosome system is essential for broadening our understanding of a multi-enzyme complex, considered to be one of the most efficient systems for plant cell wall polysaccharide degradation in nature. Following bioinformatic analysis, the second tandem module of RflaF_05439 was cloned and its selenium-labeled derivative was expressed and crystallized. The crystals belong to space group P21 with unit-cell parameters of a = 65.81, b = 60.61, c = 66.13 Å, β = 107.66° and contain two protein molecules in the asymmetric unit. The crystal structure was determined at 1.38-Å resolution by X-ray diffraction using the single-wavelength anomalous dispersion (SAD) method and was refined to Rfactor and Rfree of 0.127 and 0.152 respectively. The protein molecule mainly comprises a β-sheet flanked by short α-helixes, and a globular α-helical domain. The structure was found to be structurally similar to members of the NlpC/P60 superfamily of cysteine peptidases. The 3D structure of the second repeat of the RflaF_05439 enabled us to propose a role for the currently undefined function of this protein. Its putative function as a cysteine peptidase is inferred from in silico structural homology studies. It is therefore apparent that cellulosomes integrate proteins with other functions in addition to the classic well-defined carbohydrate active enzymes.

  • Organizational Affiliation

    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
A, B
246Ruminococcus flavefaciensMutation(s): 0 
Gene Names: NlpC/P60_2
Find proteins for M9MMP4 (Ruminococcus flavefaciens)
Explore M9MMP4 
Go to UniProtKB:  M9MMP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM9MMP4
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
Query on CCS
A, B
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 1.38 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.127 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.811α = 90
b = 60.605β = 107.66
c = 66.126γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DNAdata collection
DENZOdata reduction
SHELXEmodel building

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description