|
|
| Line 3: |
Line 3: |
| | <StructureSection load='5kdu' size='340' side='right'caption='[[5kdu]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='5kdu' size='340' side='right'caption='[[5kdu]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5kdu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clop1 Clop1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KDU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KDU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5kdu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens_ATCC_13124 Clostridium perfringens ATCC 13124]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KDU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KDU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene>, <scene name='pdbligand=TNR:O-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSYL)-L-SERINE'>TNR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5kd2|5kd2]], [[5kd5|5kd5]], [[5kd8|5kd8]], [[5kdj|5kdj]], [[5kdn|5kdn]], [[5kds|5kds]], [[5kdv|5kdv]], [[5kdw|5kdw]], [[5kdx|5kdx]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</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">CPF_1489 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=195103 CLOP1])</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5kdu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdu OCA], [https://pdbe.org/5kdu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kdu RCSB], [https://www.ebi.ac.uk/pdbsum/5kdu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdu ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5kdu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdu OCA], [http://pdbe.org/5kdu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kdu RCSB], [http://www.ebi.ac.uk/pdbsum/5kdu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdu ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A0A0H2YN38_CLOP1 A0A0H2YN38_CLOP1] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 22: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Clop1]] | + | [[Category: Clostridium perfringens ATCC 13124]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Boraston, A B]] | + | [[Category: Boraston AB]] |
| - | [[Category: Ficko-Blean, E]] | + | [[Category: Ficko-Blean E]] |
| - | [[Category: Noach, I]] | + | [[Category: Noach I]] |
| - | [[Category: Stuart, C]] | + | [[Category: Stuart C]] |
| - | [[Category: Glycopeptidase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: O-glycan]]
| + | |
| - | [[Category: Pf13402]]
| + | |
| Structural highlights
5kdu is a 1 chain structure with sequence from Clostridium perfringens ATCC 13124. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
A0A0H2YN38_CLOP1
Publication Abstract from PubMed
The vast majority of proteins are posttranslationally altered, with the addition of covalently linked sugars (glycosylation) being one of the most abundant modifications. However, despite the hydrolysis of protein peptide bonds by peptidases being a process essential to all life on Earth, the fundamental details of how peptidases accommodate posttranslational modifications, including glycosylation, has not been addressed. Through biochemical analyses and X-ray crystallographic structures we show that to hydrolyze their substrates, three structurally related metallopeptidases require the specific recognition of O-linked glycan modifications via carbohydrate-specific subsites immediately adjacent to their peptidase catalytic machinery. The three peptidases showed selectivity for different glycans, revealing protein-specific adaptations to particular glycan modifications, yet always cleaved the peptide bond immediately preceding the glycosylated residue. This insight builds upon the paradigm of how peptidases recognize substrates and provides a molecular understanding of glycoprotein degradation.
Recognition of protein-linked glycans as a determinant of peptidase activity.,Noach I, Ficko-Blean E, Pluvinage B, Stuart C, Jenkins ML, Brochu D, Buenbrazo N, Wakarchuk W, Burke JE, Gilbert M, Boraston AB Proc Natl Acad Sci U S A. 2017 Jan 17. pii: 201615141. doi:, 10.1073/pnas.1615141114. PMID:28096352[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Noach I, Ficko-Blean E, Pluvinage B, Stuart C, Jenkins ML, Brochu D, Buenbrazo N, Wakarchuk W, Burke JE, Gilbert M, Boraston AB. Recognition of protein-linked glycans as a determinant of peptidase activity. Proc Natl Acad Sci U S A. 2017 Jan 17. pii: 201615141. doi:, 10.1073/pnas.1615141114. PMID:28096352 doi:http://dx.doi.org/10.1073/pnas.1615141114
|
