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3vny

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Current revision (08:41, 20 March 2024) (edit) (undo)
 
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<StructureSection load='3vny' size='340' side='right'caption='[[3vny]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
<StructureSection load='3vny' size='340' side='right'caption='[[3vny]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vny]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acic5 Acic5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VNY FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3vny]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acidobacterium_capsulatum_ATCC_51196 Acidobacterium capsulatum ATCC 51196]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VNY 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.5&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vnz|3vnz]], [[3vo0|3vo0]]</div></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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ACP_2665 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=240015 ACIC5])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-glucuronidase Beta-glucuronidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.31 3.2.1.31] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vny OCA], [https://pdbe.org/3vny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vny RCSB], [https://www.ebi.ac.uk/pdbsum/3vny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vny 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=3vny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vny OCA], [https://pdbe.org/3vny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vny RCSB], [https://www.ebi.ac.uk/pdbsum/3vny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vny 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/C1F2K5_ACIC5 C1F2K5_ACIC5]
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We present the first structure of a glycoside hydrolase family 79 beta-glucuronidase from Acidobacterium capsulatum, both as a product complex with beta-D-glucuronic acid (GlcA) and as its trapped covalent 2-fluoroglucuronyl intermediate. This enzyme consists of a catalytic (beta/alpha)(8)-barrel domain and a beta-domain with irregular Greek key motifs that is of unknown function. The enzyme showed beta-glucuronidase activity and trace levels of beta-glucosidase and beta-xylosidase activities. In conjunction with mutagenesis studies, these structures identify the catalytic residues as Glu(173) (acid base) and Glu(287) (nucleophile), consistent with the retaining mechanism demonstrated by (1)H NMR analysis. Glu(45), Tyr(243), Tyr(292)-Gly(294), and Tyr(334) form the catalytic pocket and provide substrate discrimination. Consistent with this, the Y292A mutation, which affects the interaction between the main chains of Gln(293) and Gly(294) and the GlcA carboxyl group, resulted in significant loss of beta-glucuronidase activity while retaining the side activities at wild-type levels. Likewise, although the beta-glucuronidase activity of the Y334F mutant is ~200-fold lower (k(cat)/K(m)) than that of the wild-type enzyme, the beta-glucosidase activity is actually 3 times higher and the beta-xylosidase activity is only 2.5-fold lower than the equivalent parameters for wild type, consistent with a role for Tyr(334) in recognition of the C6 position of GlcA. The involvement of Glu(45) in discriminating against binding of the O-methyl group at the C4 position of GlcA is revealed in the fact that the E45D mutant hydrolyzes PNP-beta-GlcA approximately 300-fold slower (k(cat)/K(m)) than does the wild-type enzyme, whereas 4-O-methyl-GlcA-containing oligosaccharides are hydrolyzed only 7-fold slower.
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Structural and biochemical characterization of glycoside hydrolase family 79 beta-glucuronidase from Acidobacterium capsulatum.,Michikawa M, Ichinose H, Momma M, Biely P, Jongkees S, Yoshida M, Kotake T, Tsumuraya Y, Withers SG, Fujimoto Z, Kaneko S J Biol Chem. 2012 Apr 20;287(17):14069-77. Epub 2012 Feb 24. PMID:22367201<ref>PMID:22367201</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 3vny" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Glucuronisidase 3D structures|Glucuronisidase 3D structures]]
*[[Glucuronisidase 3D structures|Glucuronisidase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Acic5]]
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[[Category: Acidobacterium capsulatum ATCC 51196]]
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[[Category: Beta-glucuronidase]]
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[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Biely, P]]
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[[Category: Biely P]]
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[[Category: Fujimoto, Z]]
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[[Category: Fujimoto Z]]
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[[Category: Ichinose, H]]
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[[Category: Ichinose H]]
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[[Category: Kaneko, S]]
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[[Category: Kaneko S]]
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[[Category: Kotake, Y]]
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[[Category: Kotake Y]]
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[[Category: Michikawa, M]]
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[[Category: Michikawa M]]
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[[Category: Momma, M]]
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[[Category: Momma M]]
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[[Category: Tsumuraya, Y]]
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[[Category: Tsumuraya Y]]
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[[Category: Yoshida, M]]
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[[Category: Yoshida M]]
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[[Category: Glycoside hydrolase family 79]]
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[[Category: Greek-key]]
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[[Category: Hydrolase]]
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[[Category: Tim barrel]]
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Current revision

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum

PDB ID 3vny

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