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| | <StructureSection load='5a56' size='340' side='right'caption='[[5a56]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='5a56' size='340' side='right'caption='[[5a56]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5a56]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Strpn Strpn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5A56 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5a56]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_TIGR4 Streptococcus pneumoniae TIGR4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5A56 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MGC:ALPHA-METHYL-N-ACETYL-D-GALACTOSAMINE'>MGC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5a55|5a55]], [[5a57|5a57]], [[5a58|5a58]], [[5a59|5a59]], [[5a5a|5a5a]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MGC:ALPHA-METHYL-N-ACETYL-D-GALACTOSAMINE'>MGC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-alpha-N-acetylgalactosaminidase Endo-alpha-N-acetylgalactosaminidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.97 3.2.1.97] </span></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=5a56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a56 OCA], [https://pdbe.org/5a56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5a56 RCSB], [https://www.ebi.ac.uk/pdbsum/5a56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5a56 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=5a56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a56 OCA], [http://pdbe.org/5a56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5a56 RCSB], [http://www.ebi.ac.uk/pdbsum/5a56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5a56 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/GH101_STRPN GH101_STRPN]] Is involved in the breakdown of mucin-type O-linked glycans. Specifically removes the T-antigen disaccharide (Gal-beta-1,3-GalNAc-alpha) from extracellular host glycoproteins. Is representative of a broadly important class of virulence factors (By similarity). | + | [https://www.uniprot.org/uniprot/GH101_STRPN GH101_STRPN] Is involved in the breakdown of mucin-type O-linked glycans. Specifically removes the T-antigen disaccharide (Gal-beta-1,3-GalNAc-alpha) from extracellular host glycoproteins. Is representative of a broadly important class of virulence factors (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Endo-alpha-N-acetylgalactosaminidase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Strpn]] | + | [[Category: Streptococcus pneumoniae TIGR4]] |
| - | [[Category: Boraston, A B]] | + | [[Category: Boraston AB]] |
| - | [[Category: Deng, L]] | + | [[Category: Deng L]] |
| - | [[Category: Gregg, K J]] | + | [[Category: Gregg KJ]] |
| - | [[Category: Suits, M D.L]] | + | [[Category: Suits MDL]] |
| - | [[Category: Vocadlo, D J]] | + | [[Category: Vocadlo DJ]] |
| - | [[Category: Endo-beta-n-acetylgalactosaminidase]]
| + | |
| - | [[Category: Gh101]]
| + | |
| - | [[Category: Glycoside hydrolase family 101]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Mucin degradation]]
| + | |
| - | [[Category: T-antigen]]
| + | |
| Structural highlights
5a56 is a 1 chain structure with sequence from Streptococcus pneumoniae TIGR4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.8Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
GH101_STRPN Is involved in the breakdown of mucin-type O-linked glycans. Specifically removes the T-antigen disaccharide (Gal-beta-1,3-GalNAc-alpha) from extracellular host glycoproteins. Is representative of a broadly important class of virulence factors (By similarity).
Publication Abstract from PubMed
O-linked glycosylation is one of the most abundant post-translational modifications of proteins. Within the secretory pathway of higher eukaryotes, the core of these glycans is frequently an N-acetylgalactosamine residue that is alpha-linked to serine or threonine residues. Glycoside hydrolases in family 101 are presently the only known enzymes to be able to hydrolyze this glycosidic linkage. Here we determine the high-resolution structures of the catalytic domain comprising a fragment of GH101 from Streptococcus pneumoniae TIGR4, SpGH101, in the absence of carbohydrate, and in complex with reaction products, inhibitor, and substrate analogues. Upon substrate binding, a tryptophan lid (residues 724-WNW-726) closes on the substrate. The closing of this lid fully engages the substrate in the active site with D764 positioned directly beneath C1 of the sugar residue bound within the -1 subsite, consistent with its proposed role as the catalytic nucleophile. In all of the bound forms of the enzyme, however, the proposed catalytic acid/base residue was found to be too distant from the glycosidic oxygen (>4.3 A) to serve directly as a general catalytic acid/base residue and thereby facilitate cleavage of the glycosidic bond. These same complexes, however, revealed a structurally conserved water molecule positioned between the catalytic acid/base and the glycosidic oxygen. On the basis of these structural observations we propose a new variation of the retaining glycoside hydrolase mechanism wherein the intervening water molecule enables a Grotthuss proton shuttle between E796 and the glycosidic oxygen, permitting this residue to serve as the general acid/base catalytic residue.
Structural analysis of a family 101 glycoside hydrolase in complex with carbohydrates reveals insights into its mechanism.,Gregg KJ, Suits MD, Deng L, Vocadlo DJ, Boraston AB J Biol Chem. 2015 Aug 24. pii: jbc.M115.680470. PMID:26304114[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Gregg KJ, Suits MD, Deng L, Vocadlo DJ, Boraston AB. Structural analysis of a family 101 glycoside hydrolase in complex with carbohydrates reveals insights into its mechanism. J Biol Chem. 2015 Aug 24. pii: jbc.M115.680470. PMID:26304114 doi:http://dx.doi.org/10.1074/jbc.M115.680470
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