title: Crystal structure of an uncommon cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors: Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel.
authors: Maly
authors: M
authors: Levy-Assaraf
authors: Milana
authors: M
authors: Voronov-Goldman
authors: Inna
authors: I
authors: Rozman Grinberg
authors: Gloria
authors: G
authors: Weiserman
authors: Linda J W
authors: LJ
authors: Shimon
authors: Sadanari
authors: S
authors: Jindou
authors: Ilya
authors: I
authors: Borovok
authors: Bryan A
authors: BA
authors: White
authors: Edward A
authors: EA
authors: Bayer
authors: Raphael
authors: R
authors: Lamed
authors: Felix
authors: F
authors: Frolow
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D020134:Catalytic Domain; D044603:Cellulosomes / Q000737:chemistry*; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010206:Papain / Q000737:chemistry*; D011487:Protein Conformation; D045857:Ruminococcus / Q000737:chemistry* / Q000201:enzymology*; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D010206:Papain