6QDI

anti-sigma factor domain-containing protein from Clostridium clariflavum

Summary for 6QDI

• Entry DOI: 10.2210/pdb6qdi/pdb
• Descriptor: PA14 domain-containing protein, 1,2-ETHANEDIOL, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: biomass sensing, cellulosome, sigma factors, anti-sigma factors, rsgi, sigi, sugar binding protein
• Biological source: Clostridium clariflavum
• Total number of polymer chains: 1
• Total formula weight: 34221.53

Authors

Voronov, M.,Bayer, E.A.,Livnah, O. (deposition date: 2019-01-01, release date: 2019-06-12, Last modification date: 2024-05-15)

Primary citation

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.
Distinctive ligand-binding specificities of tandem PA14 biomass-sensory elements from Clostridium thermocellum and Clostridium clariflavum.
Proteins, 87:917-930, 2019

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 ) factors that have cognate membrane-associated anti-σ 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 -dependent C. clariflavum promoter sequence correlates with binding of RsgI4_PA14 to xylan and was identified in genes encoding xylanases, whereas the σ -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 ) 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.

PubMed: 31162722
DOI: 10.1002/prot.25753

Experimental method

X-RAY DIFFRACTION (1.13 Å)