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6r5a

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Revision as of 06:24, 7 August 2019

Crystal structure of PPEP-1(W103F)

Structural highlights

6r5a is a 2 chain structure with sequence from "bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	zmp1, ppep-1, CD630_28300 ("Bacillus difficilis" Hall and O'Toole 1935)
Activity:	Pro-Pro endopeptidase, with EC number 3.4.24.89
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PPEP1_PEPD6] Zinc-dependent endoprotease with a unique preference for proline residues surrounding the scissile bond. Exhibits a high preference for an asparagine at the P2 position and hydrophobic residues (Val, Ile, Leu) at the P3 position. Efficiently cleaves the LPXTG cell surface proteins CD630_28310 and CD630_32460 at multiple cleavage sites in vivo. Has a role in the regulation of C.difficile adhesion versus motility by cleaving surface adhesion proteins such as the collagen binding protein CD630_28310, and is important for efficient infection. 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 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] ^[3] ^[4]

Publication Abstract from PubMed

Pro-Pro endopeptidase-1 (PPEP-1) is a secreted metalloprotease from the bacterial pathogen Clostridium difficile that cleaves two endogenous adhesion proteins. PPEP-1 is therefore important for bacterial motility and hence for efficient gut colonization during infection. PPEP-1 exhibits a unique specificity for Pro-Pro peptide bonds within the consensus sequence VNP downward arrowPVP. In this study, we combined information from crystal and NMR structures with mutagenesis and enzyme kinetics to investigate the mechanism and substrate specificity of PPEP-1. Our analyses revealed that the substrate-binding cleft of PPEP-1 is shaped complementary to the major conformation of the substrate in solution. We found that it possesses features that accept a tertiary amide and help discriminate P1' residues by their amide hydrogen bond-donating potential. We also noted that residues Lys-101, Trp-103, and Glu-184 are crucial for proteolytic activity. Upon substrate binding, these residues position a flexible loop over the substrate-binding cleft and modulate the second coordination sphere of the catalytic zinc ion. On the basis of these findings, we propose an induced-fit model in which pre-structured substrates are recognized, followed by substrate positioning within the active-site cleft and a concomitant increase in the Lewis acidity of the catalytic Zn2+ ion. In conclusion, our findings provide detailed structural and mechanistic insights into the substrate recognition and specificity of PPEP-1 from the common gut pathogen Clostridium difficile.

Molecular determinants of the mechanism and substrate specificity of Clostridium difficile proline-proline endopeptidase-1.,Pichlo C, Juetten L, Wojtalla F, Schacherl M, Diaz D, Baumann U J Biol Chem. 2019 Jun 10. pii: RA119.009029. doi: 10.1074/jbc.RA119.009029. PMID:31182482^[5]

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
↑ Peltier J, Shaw HA, Couchman EC, Dawson LF, Yu L, Choudhary JS, Kaever V, Wren BW, Fairweather NF. Cyclic diGMP regulates production of sortase substrates of Clostridium difficile and their surface exposure through ZmpI protease-mediated cleavage. J Biol Chem. 2015 Oct 2;290(40):24453-69. doi: 10.1074/jbc.M115.665091. Epub 2015, Aug 17. PMID:26283789 doi:http://dx.doi.org/10.1074/jbc.M115.665091
↑ Hensbergen PJ, Klychnikov OI, Bakker D, Dragan I, Kelly ML, Minton NP, Corver J, Kuijper EJ, Drijfhout JW, van Leeuwen HC. Clostridium difficile secreted Pro-Pro endopeptidase PPEP-1 (ZMP1/CD2830) modulates adhesion through cleavage of the collagen binding protein CD2831. FEBS Lett. 2015 Dec 21;589(24 Pt B):3952-8. doi: 10.1016/j.febslet.2015.10.027., Epub 2015 Oct 29. PMID:26522134 doi:http://dx.doi.org/10.1016/j.febslet.2015.10.027
↑ Pichlo C, Juetten L, Wojtalla F, Schacherl M, Diaz D, Baumann U. Molecular determinants of the mechanism and substrate specificity of Clostridium difficile proline-proline endopeptidase-1. J Biol Chem. 2019 Jun 10. pii: RA119.009029. doi: 10.1074/jbc.RA119.009029. PMID:31182482 doi:http://dx.doi.org/10.1074/jbc.RA119.009029

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/6r5a"

@@ Line 3: / Line 3: @@
 <StructureSection load='6r5a' size='340' side='right'caption='[[6r5a]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6r5a]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R5A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R5A FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6r5a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R5A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R5A FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">zmp1, ppep-1, CD630_28300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1496 "Bacillus difficilis" Hall and O'Toole 1935])</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=6r5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r5a OCA], [http://pdbe.org/6r5a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r5a RCSB], [http://www.ebi.ac.uk/pdbsum/6r5a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r5a ProSAT]</span></td></tr>
@@ Line 23: / Line 24: @@
 __TOC__
 </StructureSection>
+[[Category: Bacillus difficilis hall and o'toole 1935]]
 [[Category: Large Structures]]
 [[Category: Pro-Pro endopeptidase]]

6r5a

From Proteopedia

Revision as of 06:24, 7 August 2019

Crystal structure of PPEP-1(W103F)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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