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| | <StructureSection load='2wda' size='340' side='right'caption='[[2wda]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='2wda' size='340' side='right'caption='[[2wda]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2wda]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"actinomyces_violaceus-ruber"_(sic)_waksman_and_curtis_1916 "actinomyces violaceus-ruber" (sic) waksman and curtis 1916]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WDA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WDA FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2wda]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_violaceoruber Streptomyces violaceoruber]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WDA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WDA FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ASG:2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE'>ASG</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2wco|2wco]], [[2x03|2x03]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASG:2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE'>ASG</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Hyaluronate_lyase Hyaluronate lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.1 4.2.2.1] </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=2wda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wda OCA], [https://pdbe.org/2wda PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wda RCSB], [https://www.ebi.ac.uk/pdbsum/2wda PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wda ProSAT]</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=2wda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wda OCA], [https://pdbe.org/2wda PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wda RCSB], [https://www.ebi.ac.uk/pdbsum/2wda PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wda ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/O86516_STRCO O86516_STRCO] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Hyaluronate lyase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Black, G W]] | + | [[Category: Streptomyces violaceoruber]] |
| - | [[Category: Davies, G J]] | + | [[Category: Black GW]] |
| - | [[Category: Elmabrouk, Z H]] | + | [[Category: Davies GJ]] |
| - | [[Category: Smith, N L]] | + | [[Category: Elmabrouk ZH]] |
| - | [[Category: Taylor, E J]] | + | [[Category: Smith NL]] |
| - | [[Category: Turkenburg, J P]] | + | [[Category: Taylor EJ]] |
| - | [[Category: Vincent, F]] | + | [[Category: Turkenburg JP]] |
| - | [[Category: Chondroitin lyase]]
| + | [[Category: Vincent F]] |
| - | [[Category: Family 8]]
| + | |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
2wda is a 1 chain structure with sequence from Streptomyces violaceoruber. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.3Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
O86516_STRCO
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Bacterial enzymatic degradation of glycosaminoglycans such as hyaluronan and chondroitin is facilitated by polysaccharide lyases. Family 8 polysaccharide lyase (PL8) enzymes contain at least two domains: one predominantly composed of alpha-helices, the alpha-domain, and another predominantly composed of beta-sheets, the beta-domain. Simulation flexibility analyses indicate that processive exolytic cleavage of hyaluronan, by PL8 hyaluronate lyases, is likely to involve an interdomain shift, resulting in the opening/closing of the substrate-binding cleft between the alpha- and beta-domains, facilitating substrate translocation. Here, the Streptomyces coelicolor A3(2) PL8 enzyme was recombinantly expressed in and purified from Escherichia coli and biochemically characterized as a hyaluronate lyase. By using X-ray crystallography its structure was solved in complex with hyaluronan and chondroitin disaccharides. These findings show key catalytic interactions made by the different substrates, and on comparison with all other PL8 structures reveals that the substrate-binding cleft of the S. coelicolor enzyme is highly occluded. A third structure of the enzyme, harboring a mutation of the catalytic tyrosine, created via site-directed mutagenesis, interestingly revealed an interdomain shift that resulted in the opening of the substrate-binding cleft. These results add further support to the proposed processive mechanism of action of PL8 hyaluronate lyases and may indicate that the mechanism of action is likely to be universally used by PL8 hyaluronate lyases. Proteins 2011. (c) 2010 Wiley-Liss, Inc.
Crystal structures of a family 8 polysaccharide lyase reveal open and highly occluded substrate-binding cleft conformations.,Elmabrouk ZH, Vincent F, Zhang M, Smith NL, Turkenburg JP, Charnock SJ, Black GW, Taylor EJ Proteins. 2011 Mar;79(3):965-74. doi: 10.1002/prot.22938. Epub 2010 Dec, 18. PMID:21287626[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Elmabrouk ZH, Vincent F, Zhang M, Smith NL, Turkenburg JP, Charnock SJ, Black GW, Taylor EJ. Crystal structures of a family 8 polysaccharide lyase reveal open and highly occluded substrate-binding cleft conformations. Proteins. 2011 Mar;79(3):965-74. doi: 10.1002/prot.22938. Epub 2010 Dec, 18. PMID:21287626 doi:10.1002/prot.22938
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