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Yorodumi- SASDAM5: CD27L (C238R) (Clostridium difficile bacteriophage 27 endolysin C... -
+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDAM5 |
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Sample | CD27L (C238R)
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Biological species | Clostridioides difficile (bacteria) |
Citation | Journal: PLoS Pathog / Year: 2014 Title: The CD27L and CTP1L endolysins targeting Clostridia contain a built-in trigger and release factor. Authors: Matthew Dunne / Haydyn D T Mertens / Vasiliki Garefalaki / Cy M Jeffries / Andrew Thompson / Edward A Lemke / Dmitri I Svergun / Melinda J Mayer / Arjan Narbad / Rob Meijers / Abstract: The bacteriophage ΦCD27 is capable of lysing Clostridium difficile, a pathogenic bacterium that is a major cause for nosocomial infection. A recombinant CD27L endolysin lyses C. difficile in vitro, ...The bacteriophage ΦCD27 is capable of lysing Clostridium difficile, a pathogenic bacterium that is a major cause for nosocomial infection. A recombinant CD27L endolysin lyses C. difficile in vitro, and represents a promising alternative as a bactericide. To better understand the lysis mechanism, we have determined the crystal structure of an autoproteolytic fragment of the CD27L endolysin. The structure covers the C-terminal domain of the endolysin, and represents a novel fold that is identified in a number of lysins that target Clostridia bacteria. The structure indicates endolysin cleavage occurs at the stem of the linker connecting the catalytic domain with the C-terminal domain. We also solved the crystal structure of the C-terminal domain of a slow cleaving mutant of the CTP1L endolysin that targets C. tyrobutyricum. Two distinct dimerization modes are observed in the crystal structures for both endolysins, despite a sequence identity of only 22% between the domains. The dimers are validated to be present for the full length protein in solution by right angle light scattering, small angle X-ray scattering and cross-linking experiments using the cross-linking amino acid p-benzoyl-L-phenylalanine (pBpa). Mutagenesis on residues contributing to the dimer interfaces indicates that there is a link between the dimerization modes and the autocleavage mechanism. We show that for the CTP1L endolysin, there is a reduction in lysis efficiency that is proportional to the cleavage efficiency. We propose a model for endolysin triggering, where the extended dimer presents the inactive state, and a switch to the side-by-side dimer triggers the cleavage of the C-terminal domain. This leads to the release of the catalytic portion of the endolysin, enabling the efficient digestion of the bacterial cell wall. |
Contact author |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Models
Model #124 | Type: dummy / Software: (0.9) / Radius of dummy atoms: 3.10 A / Symmetry: P2 / Chi-square value: 0.919681 Search similar-shape structures of this assembly by Omokage search (details) |
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Model #126 | Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 0.876096 Search similar-shape structures of this assembly by Omokage search (details) |
Model #127 | Type: mix / Software: (2.0) / Radius of dummy atoms: 1.90 A Comment: Only terminal residues added with EOM to core based on PDB ID: 4CU5 and 3QAY Chi-square value: 16.345849 Search similar-shape structures of this assembly by Omokage search (details) |
-Sample
Sample | Name: CD27L (C238R) / Sample MW: 64.2 kDa / Specimen concentration: 1.00-8.50 / Concentration method: A280 |
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Buffer | Name: 20 mM HEPES 500 mM NaCl / pH: 7.5 / Composition: NaCl 500.000 mM |
Entity #95 | Name: CD27L(C238R) / Type: protein Description: Clostridium difficile bacteriophage 27 endolysin C238R mutant Formula weight: 32.1 / Num. of mol.: 2 / Source: Clostridioides difficile Sequence: MGSSHHHHHH SSGLVPRGSH MKICITVGHS ILKSGACTSA DGVVNEYQYN KSLAPVLADT FRKEGHKVDV IIsPEKQFKT KNEEKSYKIP RVNSGGYDLL IELHLNASNG QGKGSEVLYY SNKGLEYATR ICDKLGTVFK NRGAKLDKRL YILNSSKPTA VLIESFFCDN ...Sequence: MGSSHHHHHH SSGLVPRGSH MKICITVGHS ILKSGACTSA DGVVNEYQYN KSLAPVLADT FRKEGHKVDV IIsPEKQFKT KNEEKSYKIP RVNSGGYDLL IELHLNASNG QGKGSEVLYY SNKGLEYATR ICDKLGTVFK NRGAKLDKRL YILNSSKPTA VLIESFFCDN KEDYDKAKKL GHEGIAKLIV EGVLNKNINN EGVKQMYKHT IVYDGEVDKI SATVVGWGYN DGKILICDIK DYVPGQTQNL YVVGGGAREK ISSITKEKFI MIKGNDRFDT LYKALDFIN |
-Experimental information
Beam | Instrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.12 Å / Dist. spec. to detc.: 3.1 mm | ||||||||||||||||||||||||||||||
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Detector | Name: Pilatus 2M | ||||||||||||||||||||||||||||||
Scan | Title: CD27L (C238R) / Measurement date: Jun 21, 2013 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /
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Distance distribution function P(R) | Sofotware P(R): GNOM 4.5a / Number of points: 342 /
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Result | Type of curve: merged / Standard: BSA
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