3gh4: Difference between revisions
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==Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12== | ==Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12== | ||
<StructureSection load='3gh4' size='340' side='right' caption='[[3gh4]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='3gh4' size='340' side='right'caption='[[3gh4]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3gh4]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3gh4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paesp Paesp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GH4 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gh5|3gh5]], [[3gh7|3gh7]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gh5|3gh5]], [[3gh7|3gh7]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Hex1 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Hex1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=58172 PAESP])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-N-acetylhexosaminidase Beta-N-acetylhexosaminidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.52 3.2.1.52] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gh4 OCA], [https://pdbe.org/3gh4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gh4 RCSB], [https://www.ebi.ac.uk/pdbsum/3gh4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gh4 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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==See Also== | ==See Also== | ||
*[[Beta-Hexosaminidase|Beta-Hexosaminidase]] | *[[Beta-Hexosaminidase|Beta-Hexosaminidase]] | ||
*[[Beta-Hexosaminidase 3D structures|Beta-Hexosaminidase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Beta-N-acetylhexosaminidase]] | [[Category: Beta-N-acetylhexosaminidase]] | ||
[[Category: Large Structures]] | |||
[[Category: Paesp]] | [[Category: Paesp]] | ||
[[Category: Ishii, R]] | [[Category: Ishii, R]] | ||
Revision as of 11:05, 9 March 2022
Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12
Structural highlights
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 PubMedWe report the molecular cloning and characterization of two novel beta-N-acetylhexosaminidases (beta-HEX, EC 3.2.1.52) from Paenibacillus sp. strain TS12. The two beta-HEXs (Hex1 and Hex2) were 70% identical in primary structure, and the N-terminal region of both enzymes showed significant similarity with beta-HEXs belonging to glycoside hydrolase family 20 (GH20). Interestingly, however, the C-terminal region of Hex1 and Hex2 shared no sequence similarity with the GH20 beta-HEXs or other known proteins. Both recombinant enzymes, expressed in Escherichia coli BL21(DE3), hydrolyzed the beta-N-acetylhexosamine linkage of chitooligosaccharides and glycosphingolipids such as asialo GM2 and Gb4Cer in the absence of detergent. However, the enzyme was not able to hydrolyze GM2 ganglioside in the presence or in the absence of detergent. We determined three crystal structures of Hex1; the Hex1 deletion mutant Hex1-DeltaC at a resolution of 1.8 A; Hex1-DeltaC in complex with beta-N-acetylglucosamine at 1.6 A; and Hex1-DeltaC in complex with beta-N-acetylgalactosamine at 1.9 A. We made a docking model of Hex1-DeltaC with GM2 oligosaccharide, revealing that the sialic acid residue of GM2 could hinder access of the substrate to the active site cavity. This is the first report describing the molecular cloning, characterization and X-ray structure of a procaryotic beta-HEX capable of hydrolyzing glycosphingolipids. Molecular cloning and crystal structural analysis of a novel beta-N-acetylhexosaminidase from Paenibacillus sp. TS12 capable of degrading glycosphingolipids.,Sumida T, Ishii R, Yanagisawa T, Yokoyama S, Ito M J Mol Biol. 2009 Sep 11;392(1):87-99. Epub 2009 Jun 12. PMID:19524595[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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