6QDI

anti-sigma factor domain-containing protein from Clostridium clariflavum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Distinctive ligand-binding specificities of tandem PA14 biomass-sensory elements from Clostridium thermocellum and Clostridium clariflavum.

Grinberg, I.R.Yaniv, O.de Ora, L.O.Munoz-Gutierrez, I.Hershko, A.Livnah, O.Bayer, E.A.Borovok, I.Frolow, F.Lamed, R.Voronov-Goldman, M.

(2019) Proteins 87: 917-930

  • DOI: 10.1002/prot.25753
  • Primary Citation of Related Structures:  
    6QE7, 6QDI

  • PubMed Abstract: 
  • Cellulolytic clostridia use a highly efficient cellulosome system to degrade polysaccharides. To regulate genes encoding enzymes of the multi-enzyme cellulosome complex, certain clostridia contain alternative sigma I (σ I ) factors that have cognate membrane-associated anti-σ I factors (RsgIs) which act as polysaccharide sensors ...

    Cellulolytic clostridia use a highly efficient cellulosome system to degrade polysaccharides. To regulate genes encoding enzymes of the multi-enzyme cellulosome complex, certain clostridia contain alternative sigma I (σ I ) factors that have cognate membrane-associated anti-σ I factors (RsgIs) which act as polysaccharide sensors. In this work, we analyzed the structure-function relationship of the extracellular sensory elements of Clostridium (Ruminiclostridium) thermocellum and Clostridium clariflavum (RsgI3 and RsgI4, respectively). These elements were selected for comparison, as each comprised two tandem PA14-superfamily motifs. The X-ray structures of the PA14 modular dyads from the two bacterial species were determined, both of which showed a high degree of structural and sequence similarity, although their binding preferences differed. Bioinformatic approaches indicated that the DNA sequence of promoter of sigI/rsgI operons represents a strong signature, which helps to differentiate binding specificity of the structurally similar modules. The σ I4 -dependent C. clariflavum promoter sequence correlates with binding of RsgI4_PA14 to xylan and was identified in genes encoding xylanases, whereas the σ I3 -dependent C. thermocellum promoter sequence correlates with RsgI3_PA14 binding to pectin and regulates pectin degradation-related genes. Structural similarity between clostridial PA14 dyads to PA14-containing proteins in yeast helped identify another crucial signature element: the calcium-binding loop 2 (CBL2), which governs binding specificity. Variations in the five amino acids that constitute this loop distinguish the pectin vs xylan specificities. We propose that the first module (PA14 A ) is dominant in directing the binding to the ligand in both bacteria. The two X-ray structures of the different PA14 dyads represent the first reported structures of tandem PA14 modules.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PA14 domain-containing proteinA295Acetivibrio clariflavusMutation(s): 0 
Gene Names: Clocl_2747
UniProt
Find proteins for G8M2Z2 (Hungateiclostridium clariflavum (strain DSM 19732 / NBRC 101661 / EBR45))
Explore G8M2Z2 
Go to UniProtKB:  G8M2Z2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.6α = 90
b = 41.43β = 100.35
c = 73.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references