3eka: Difference between revisions
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==Crystal structure of the complex of hyaluranidase trimer with ascorbic acid at 3.1 A resolution reveals the locations of three binding sites== | ==Crystal structure of the complex of hyaluranidase trimer with ascorbic acid at 3.1 A resolution reveals the locations of three binding sites== | ||
<StructureSection load='3eka' size='340' side='right' caption='[[3eka]], [[Resolution|resolution]] 3.10Å' scene=''> | <StructureSection load='3eka' size='340' side='right'caption='[[3eka]], [[Resolution|resolution]] 3.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3eka]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3eka]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pyogenes Streptococcus pyogenes]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pk1 2pk1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EKA FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASC:ASCORBIC+ACID'>ASC</scene></td></tr> | |||
<tr id=' | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3eka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eka OCA], [https://pdbe.org/3eka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eka RCSB], [https://www.ebi.ac.uk/pdbsum/3eka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eka ProSAT]</span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q9A0M7_STRP1 Q9A0M7_STRP1] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ek/3eka_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ek/3eka_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/ | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3eka ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3eka" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Hyaluronidase|Hyaluronidase]] | *[[Hyaluronidase 3D structures|Hyaluronidase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Streptococcus pyogenes]] | [[Category: Streptococcus pyogenes]] | ||
[[Category: Bhakuni | [[Category: Bhakuni V]] | ||
[[Category: Ethayathulla | [[Category: Ethayathulla AS]] | ||
[[Category: Kaur | [[Category: Kaur P]] | ||
[[Category: | [[Category: Mishra P]] | ||
[[Category: | [[Category: Prem Kumar R]] | ||
[[Category: Sharma | [[Category: Sharma S]] | ||
[[Category: Singh | [[Category: Singh N]] | ||
[[Category: Singh | [[Category: Singh TP]] | ||
Latest revision as of 18:21, 1 November 2023
Crystal structure of the complex of hyaluranidase trimer with ascorbic acid at 3.1 A resolution reveals the locations of three binding sitesCrystal structure of the complex of hyaluranidase trimer with ascorbic acid at 3.1 A resolution reveals the locations of three binding sites
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedHyaluronate lyases are a class of endoglycosaminidase enzymes with a high level of complexity and heterogeneity. The main function of the Streptococcus pyogenes bacteriophage protein hyaluronate lyase, HylP2, is to degrade hyaluronan into unsaturated disaccharide units. HylP2 was cloned, over-expressed and purified to homogeneity. The recombinant HylP2 exists as a homotrimer with a molecular mass of approximately 110 kDa under physiological conditions. The HylP2 was crystallized and the crystals were soaked in two separate reservoir solutions containing ascorbic acid and lactose, respectively. The crystal structures of native HylP2 and its two complexes with ascorbic acid and lactose have been determined. HylP2 folds into four distinct domains with a central core consisting of 16 antiparallel beta-strands forming an irregular triangular tube designated as triple-stranded beta-helix. The structures of complexes show that three molecules each of ascorbic acid and lactose bind to protein at the sugar binding groove in the triple-stranded beta-helix domain. Both ascorbic acid and lactose molecules occupy almost identical subsites in the long saccharide binding groove. Both ligands are involved in several hydrogen bonded interactions at each subsite. The binding characteristics and stereochemical properties indicate that Tyr264 may be involved in the catalytic activity of HylP2. The mutation of Tyr264 to Phe264 supports this observation. Polysaccharide binding sites in hyaluronate lyase--crystal structures of native phage-encoded hyaluronate lyase and its complexes with ascorbic acid and lactose.,Mishra P, Prem Kumar R, Ethayathulla AS, Singh N, Sharma S, Perbandt M, Betzel C, Kaur P, Srinivasan A, Bhakuni V, Singh TP FEBS J. 2009 Jun;276(12):3392-402. Epub 2009 May 8. PMID:19438710[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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