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 

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:  

  • 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 <sup>I </sup> ) factors that h ...

    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 bactrerial 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 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 distinguishes the pectin versus 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. This article is protected by copyright. All rights reserved.


    Organizational Affiliation

    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel.,Outreach Research Training and Minority Science Programs, School of Biological Sciences, University of California, Irvine, California, USA.,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, Jerusalem, Israel.,Department of Biochemistry and Biophysics, Stockholm University, Sweden.,Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.,Department of Chemistry, University of California, Irvine, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PA14 domain-containing protein
A
295Hungateiclostridium clariflavum (strain DSM 19732 / NBRC 101661 / EBR45)Mutation(s): 0 
Find proteins for G8M2Z2 (Hungateiclostridium clariflavum (strain DSM 19732 / NBRC 101661 / EBR45))
Go to UniProtKB:  G8M2Z2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.146 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 104.600α = 90.00
b = 41.430β = 100.35
c = 73.310γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
AutoPROCdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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