5n12: Difference between revisions
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==Crystal structure of TCE treated rPPEP-1== | ==Crystal structure of TCE treated rPPEP-1== | ||
<StructureSection load='5n12' size='340' side='right' caption='[[5n12]], [[Resolution|resolution]] 1.38Å' scene=''> | <StructureSection load='5n12' size='340' side='right'caption='[[5n12]], [[Resolution|resolution]] 1.38Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5n12]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N12 FirstGlance]. <br> | <table><tr><td colspan='2'>[[5n12]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridioides_difficile_630 Clostridioides difficile 630]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N12 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8FH:2,2,2-tris-chloroethanol'>8FH</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8FH:2,2,2-tris-chloroethanol'>8FH</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5a0p|5a0p]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5a0p|5a0p]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">zmp1, CD630_28300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272563 Clostridioides difficile 630])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pro-Pro_endopeptidase Pro-Pro endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.89 3.4.24.89] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pro-Pro_endopeptidase Pro-Pro endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.89 3.4.24.89] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5n12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n12 OCA], [http://pdbe.org/5n12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n12 RCSB], [http://www.ebi.ac.uk/pdbsum/5n12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n12 ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5n12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n12 OCA], [http://pdbe.org/5n12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n12 RCSB], [http://www.ebi.ac.uk/pdbsum/5n12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n12 ProSAT]</span></td></tr> | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Clostridioides difficile 630]] | |||
[[Category: Large Structures]] | |||
[[Category: Pro-Pro endopeptidase]] | [[Category: Pro-Pro endopeptidase]] | ||
[[Category: Baumann, U]] | [[Category: Baumann, U]] | ||
Revision as of 09:41, 16 October 2019
Crystal structure of TCE treated rPPEP-1Crystal structure of TCE treated rPPEP-1
Structural highlights
Function[ZMP1_PEPD6] Zinc-dependent endoprotease with a preference for proline residues surrounding the scissile bond. Efficiently cleaves the LPXTG cell surface proteins CD630_28310 and CD630_32460 at multiple cleavage sites. Is also able to cleave fibronectin and fibrinogen in vitro; cleaves at the N-terminus of the beta-chain of fibrinogen. Destabilizes the fibronectin network produced by human fibroblasts. Therefore, may have a role in the regulation of C.difficile adhesion versus motility by cleaving surface adhesion proteins, and may be important in key steps of clostridial pathogenesis by degrading extracellular matrix components associated with the gut epithelial cells. To a lesser extent, IgA1, IgA2, and human HSP 90-beta, but not HSP 90-alpha, are also substrates for the enzyme. Is not active on different collagen types, casein and gelatin.[1] [2] Publication Abstract from PubMedThe identification of initial lead conditions for successful protein crystallization is crucial for structural studies using X-ray crystallography. In order to reduce the number of false-negative conditions, an emerging number of fluorescence-based methods have been developed which allow more efficient identification of protein crystals and help to distinguish them from salt crystals. Detection of the native tryptophan fluorescence of protein crystals is one of the most widely used methods. However, this method can fail owing to the properties of the crystallized protein or the chemical composition of the crystallization trials. Here, a simple, fast and cost-efficient method employing 2,2,2-trichloroethanol (TCE) has been developed. It can be performed with a standard UV-light microscope and can be applied to cases in which detection of native tryptophan fluorescence fails. In four test cases this method had no effect on the diffraction properties of the crystals and no structural changes were observed. Further evidence is provided that TCE can be added to crystallization trials during their preparation, making this method compatible with high-throughput approaches. Improved protein-crystal identification by using 2,2,2-trichloroethanol as a fluorescence enhancer.,Pichlo C, Toelzer C, Chojnacki K, Ocal S, Uthoff M, Ruegenberg S, Hermanns T, Schacherl M, Denzel MS, Hofmann K, Niefind K, Baumann U Acta Crystallogr F Struct Biol Commun. 2018 May 1;74(Pt 5):307-314. doi:, 10.1107/S2053230X18005253. Epub 2018 Apr 24. PMID:29717999[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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