5yif: Difference between revisions
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<StructureSection load='5yif' size='340' side='right'caption='[[5yif]], [[Resolution|resolution]] 2.45Å' scene=''> | <StructureSection load='5yif' size='340' side='right'caption='[[5yif]], [[Resolution|resolution]] 2.45Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5yif]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIF OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5yif]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._(in:_Bacteria) Bacillus sp. (in: Bacteria)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YIF FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8VR:(2R,4aR,6R,7R,8R,8aR)-2-methyl-6,7,8-tris(oxidanyl)-4,4a,6,7,8,8a-hexahydropyrano[3,2-d][1,3]dioxine-2-carboxylic+acid'>8VR</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]] 2.45Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8VR:(2R,4aR,6R,7R,8R,8aR)-2-methyl-6,7,8-tris(oxidanyl)-4,4a,6,7,8,8a-hexahydropyrano[3,2-d][1,3]dioxine-2-carboxylic+acid'>8VR</scene></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=5yif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yif OCA], [https://pdbe.org/5yif PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yif RCSB], [https://www.ebi.ac.uk/pdbsum/5yif PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yif ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A2B9BPQ7_BACCE A0A2B9BPQ7_BACCE] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 5yif" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5yif" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Galactosidase 3D structures|Galactosidase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Arakawa | [[Category: Arakawa T]] | ||
[[Category: Fushinobu | [[Category: Fushinobu S]] | ||
[[Category: Higuchi | [[Category: Higuchi Y]] | ||
[[Category: Takegawa | [[Category: Takegawa K]] | ||
[[Category: Tanuma | [[Category: Tanuma M]] | ||
[[Category: Yamada | [[Category: Yamada C]] | ||
Latest revision as of 11:30, 22 November 2023
Pyruvylated beta-D-galactosidase from Bacillus sp. HMA207, E163A mutant pyruvylated beta-D-galactose complexPyruvylated beta-D-galactosidase from Bacillus sp. HMA207, E163A mutant pyruvylated beta-D-galactose complex
Structural highlights
FunctionPublication Abstract from PubMedPyruvyl modification of oligosaccharides is widely seen in both prokaryotes and eukaryotes. Although the biosynthetic mechanisms of pyruvylation have been investigated, enzymes that metabolize and degrade pyruvylated oligosaccharides are not well known. Here, we searched for a pyruvylated galactose (PvGal)-releasing enzyme by screening soil samples. We identified a Bacillus strain, as confirmed by the 16S ribosomal RNA gene analysis, that exhibited PvGal-ase activity toward p-nitrophenyl-beta-D-pyruvylated galactopyranose (pNP-beta-D-PvGal). Draft genome sequencing of this strain, named HMA207, identified three candidate genes encoding potential PvGal-ases, among which only the recombinant protein encoded by ORF1119 exhibited PvGal-ase activity. Although ORF1119 protein displayed broad substrate specificity for pNP sugars, pNP-beta-D-PvGal was the most favorable substrate. The optimum pH for the ORF1119 PvGal-ase was determined as 7.5. A BLAST search suggested that ORF1119 homologs exist widely in bacteria. Among two homologs tested, BglC from Clostridium but not BglH from Bacillus showed PvGal-ase activity. Crystal structural analysis together with point mutation analysis revealed crucial amino acids for PvGal-ase activity. Moreover, ORF1119 protein catalyzed the hydrolysis of PvGal from galactomannan of Schizosaccharomyces pombe, suggesting that natural polysaccharides might be substrates of the PvGal-ase. This novel PvGal-catalyzing enzyme might be useful for glycoengineering projects to produce new oligosaccharide structures. Identification and characterization of a novel beta-D-galactosidase that releases pyruvylated galactose.,Higuchi Y, Matsufuji H, Tanuma M, Arakawa T, Mori K, Yamada C, Shofia R, Matsunaga E, Tashiro K, Fushinobu S, Takegawa K Sci Rep. 2018 Aug 13;8(1):12013. doi: 10.1038/s41598-018-30508-4. PMID:30104607[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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