6m5a

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Current revision (10:48, 27 March 2024) (edit) (undo)
 
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<StructureSection load='6m5a' size='340' side='right'caption='[[6m5a]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
<StructureSection load='6m5a' size='340' side='right'caption='[[6m5a]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6m5a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/As_1.2186 As 1.2186]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M5A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M5A FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6m5a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M5A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M5A FirstGlance]. <br>
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</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DWV93_04865 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216816 AS 1.2186])</td></tr>
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<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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=6m5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m5a OCA], [https://pdbe.org/6m5a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m5a RCSB], [https://www.ebi.ac.uk/pdbsum/6m5a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m5a 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=6m5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m5a OCA], [https://pdbe.org/6m5a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m5a RCSB], [https://www.ebi.ac.uk/pdbsum/6m5a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m5a ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/HYBA2_BIFL2 HYBA2_BIFL2] Beta-L-arabinobiosidase that removes L-arabinofuranose-beta-1,2-L-arabinofuranose disaccharide from various substrates such as carrot extensin and potato lectin. Also acts on L-arabinofuranose (Ara)-beta-1,2-Ara-beta-1,2-Ara-beta-Hyp (Ara(3)-Hyp) but not on Ara-beta-1,3-Ara-beta-1,2-Ara-beta-1,2-Ara-beta--Hyp (Ara(4)-Hyp) or Ara-beta-1,2-Ara-beta-Hyp (Ara(2)-Hyp), suggesting a specificity for unmodified Ara(3)-Hyp substrate. In the presence of 1-alkanols, shows transglycosylation activity, retaining the anomeric configuration of the arabinofuranose residue.<ref>PMID:21149454</ref>
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Enzymes acting on alpha-L-arabinofuranosides have been extensively studied; however, the structures and functions of beta-L-arabinofuranosidases are not fully understood. Three enzymes and an ABC transporter in a gene cluster of Bifidobacterium longum JCM 1217 constitute a degradation and import system of beta-L-arabinooligosaccharides on plant hydroxyproline-rich glycoproteins. An extracellular beta-L-arabinobiosidase (HypBA2) belonging to the glycoside hydrolase (GH) family 121 plays a key role in the degradation pathway by releasing beta-1,2-linked arabinofuranose disaccharide (beta-Ara2) for the specific sugar importer. Here, we present the crystal structure of the catalytic region of HypBA2 as the first three-dimensional structure of GH121 at 1.85 A resolution. The HypBA2 structure consists of a central catalytic (alpha/alpha)6 barrel domain and two flanking (N- and C-terminal) beta-sandwich domains. A pocket in the catalytic domain appears to be suitable for accommodating the beta-Ara2 disaccharide. Three acidic residues Glu383, Asp515, and Glu713, located in this pocket, are completely conserved among all members of GH121; site-directed mutagenesis analysis showed that they are essential for catalytic activity. The active site of HypBA2 was compared with those of structural homologs in other GH families: GH63 alpha-glycosidase, GH94 chitobiose phosphorylase, GH142 beta-L-arabinofuranosidase, GH78 alpha-L-rhamnosidase, and GH37 alpha,alpha-trehalase. Based on these analyses, we concluded that the three conserved residues are essential for catalysis and substrate binding. beta-L-Arabinobiosidase genes in GH121 are mainly found in the genomes of bifidobacteria and Xanthomonas species, suggesting that the cleavage and specific import system for the beta-Ara2 disaccharide on plant hydroxyproline-rich glycoproteins are shared in animal gut symbionts and plant pathogens.
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Crystal structure of beta-L-arabinobiosidase belonging to glycoside hydrolase family 121.,Saito K, Viborg AH, Sakamoto S, Arakawa T, Yamada C, Fujita K, Fushinobu S PLoS One. 2020 Jun 1;15(6):e0231513. doi: 10.1371/journal.pone.0231513., eCollection 2020. PMID:32479540<ref>PMID:32479540</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6m5a" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: As 1 2186]]
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[[Category: Bifidobacterium longum]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Arakawa, T]]
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[[Category: Arakawa T]]
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[[Category: Fujita, K]]
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[[Category: Fujita K]]
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[[Category: Fushinobu, S]]
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[[Category: Fushinobu S]]
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[[Category: Saito, K]]
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[[Category: Saito K]]
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[[Category: Yamada, C]]
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[[Category: Yamada C]]
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[[Category: Glycoside hydrolase family 121]]
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[[Category: Hydrolase]]
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Current revision

Crystal structure of GH121 beta-L-arabinobiosidase HypBA2 from Bifidobacterium longum

PDB ID 6m5a

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