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5n12

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Revision as of 06:41, 16 October 2019

Crystal structure of TCE treated rPPEP-1

Structural highlights

5n12 is a 2 chain structure with sequence from Clostridioides difficile 630. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	5a0p
Gene:	zmp1, CD630_28300 (Clostridioides difficile 630)
Activity:	Pro-Pro endopeptidase, with EC number 3.4.24.89
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 PubMed

The 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

↑ Cafardi V, Biagini M, Martinelli M, Leuzzi R, Rubino JT, Cantini F, Norais N, Scarselli M, Serruto D, Unnikrishnan M. Identification of a novel zinc metalloprotease through a global analysis of Clostridium difficile extracellular proteins. PLoS One. 2013 Nov 26;8(11):e81306. doi: 10.1371/journal.pone.0081306., eCollection 2013. PMID:24303041 doi:http://dx.doi.org/10.1371/journal.pone.0081306
↑ Hensbergen PJ, Klychnikov OI, Bakker D, van Winden VJ, Ras N, Kemp AC, Cordfunke RA, Dragan I, Deelder AM, Kuijper EJ, Corver J, Drijfhout JW, van Leeuwen HC. A novel secreted metalloprotease (CD2830) from Clostridium difficile cleaves specific proline sequences in LPXTG cell surface proteins. Mol Cell Proteomics. 2014 May;13(5):1231-44. doi: 10.1074/mcp.M113.034728. Epub, 2014 Mar 12. PMID:24623589 doi:http://dx.doi.org/10.1074/mcp.M113.034728
↑ Pichlo C, Toelzer C, Chojnacki K, Ocal S, Uthoff M, Ruegenberg S, Hermanns T, Schacherl M, Denzel MS, Hofmann K, Niefind K, Baumann U. Improved protein-crystal identification by using 2,2,2-trichloroethanol as a fluorescence enhancer. Acta Crystallogr F Struct Biol Commun. 2018 May 1;74(Pt 5):307-314. doi:, 10.1107/S2053230X18005253. Epub 2018 Apr 24. PMID:29717999 doi:http://dx.doi.org/10.1107/S2053230X18005253

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5n12"

@@ Line 1: / Line 1: @@
 ==Crystal structure of TCE treated rPPEP-1==
-<StructureSection load='5n12' size='340' side='right' caption='[[5n12]], [[Resolution|resolution]] 1.38&Aring;' scene=''>
+<StructureSection load='5n12' size='340' side='right'caption='[[5n12]], [[Resolution|resolution]] 1.38&Aring;' scene=''>
 == 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>
 <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='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>
@@ Line 24: / Line 25: @@
 __TOC__
 </StructureSection>
+[[Category: Clostridioides difficile 630]]
+[[Category: Large Structures]]
 [[Category: Pro-Pro endopeptidase]]
 [[Category: Baumann, U]]

5n12

From Proteopedia

Revision as of 06:41, 16 October 2019

Crystal structure of TCE treated rPPEP-1

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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