6d7j

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Current revision (14:33, 13 March 2024) (edit) (undo)
 
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<StructureSection load='6d7j' size='340' side='right'caption='[[6d7j]], [[Resolution|resolution]] 2.24&Aring;' scene=''>
<StructureSection load='6d7j' size='340' side='right'caption='[[6d7j]], [[Resolution|resolution]] 2.24&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6d7j]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Parabacteroides_merdae_cl03t12c32 Parabacteroides merdae cl03t12c32]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D7J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6D7J FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6d7j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Parabacteroides_merdae_CL03T12C32 Parabacteroides merdae CL03T12C32]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D7J 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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</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]] 2.24&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HMPREF1060_00403 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=999420 Parabacteroides merdae CL03T12C32])</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6d7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d7j OCA], [http://pdbe.org/6d7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d7j RCSB], [http://www.ebi.ac.uk/pdbsum/6d7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d7j ProSAT]</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=6d7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d7j OCA], [https://pdbe.org/6d7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d7j RCSB], [https://www.ebi.ac.uk/pdbsum/6d7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d7j 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/K5ZWV5_9BACT K5ZWV5_9BACT]
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beta-Glucuronidase (GUS) enzymes in the gastrointestinal tract are involved in maintaining mammalian-microbial symbiosis and can play key roles in drug efficacy and toxicity. Parabacteroides merdae GUS was identified as an abundant mini-Loop 2 (mL2) type GUS enzyme in the Human Microbiome Project gut metagenomic database. Here, we report the crystal structure of P. merdae GUS and highlight the differences between this enzyme and extant structures of gut microbial GUS proteins. We find that P. merdae GUS exhibits a distinct tetrameric quaternary structure and that the mL2 motif traces a unique path within the active site, which also includes two arginines distinctive to this GUS. We observe two states of the P. merdae GUS active site; a loop repositions itself by more than 50 A to place a functionally-relevant residue into the enzyme's catalytic site. Finally, we find that P. merdae GUS is able to bind to homo and heteropolymers of the polysaccharide alginic acid. Together, these data broaden our understanding of the structural and functional diversity in the GUS family of enzymes present in the human gut microbiome and point to specialization as an important feature of microbial GUS orthologs.
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Active site flexibility revealed in crystal structures of Parabacteroides merdae beta-glucuronidase from the human gut microbiome.,Little MS, Ervin SM, Walton WG, Tripathy A, Xu Y, Liu J, Redinbo MR Protein Sci. 2018 Dec;27(12):2010-2022. doi: 10.1002/pro.3507. Epub 2018 Oct 27. PMID:30230652<ref>PMID:30230652</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 6d7j" 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>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Parabacteroides merdae cl03t12c32]]
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[[Category: Parabacteroides merdae CL03T12C32]]
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[[Category: Little, M S]]
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[[Category: Little MS]]
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[[Category: Redinbo, M R]]
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[[Category: Redinbo MR]]
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[[Category: Bacterial enzyme]]
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[[Category: Beta-glucuronidase]]
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[[Category: Carbohydrate binding protein]]
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[[Category: Glycoside hydrolase family 2]]
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[[Category: Gus]]
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[[Category: Hydrolase]]
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Current revision

The Crystal Structure of Parabacteroides merdae Beta-Glucuronidase (GUS) with Glycerol in Active-Site

PDB ID 6d7j

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