4awd

From Proteopedia

(Difference between revisions)

Revision as of 05:48, 25 August 2022

Crystal structure of the beta-porphyranase BpGH16B (BACPLE_01689) from the human gut bacterium Bacteroides plebeius

Structural highlights

4awd is a 2 chain structure with sequence from Bacteroides plebeius. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Activity:	Beta-porphyranase, with EC number 3.2.1.178
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PORB_BACPM] Cleaves the sulfated polysaccharide porphyran at the (1->4) linkages between beta-D-galactopyranose and alpha-L-galactopyranose-6-sulfate, forming mostly the disaccharide alpha-L-galactopyranose-6-sulfate-(1->3)-beta-D-galactose. Some longer oligosaccharides of even number of residues are also observed. Inactive on the non-sulfated agarose portion of the porphyran backbone.^[1]

Publication Abstract from PubMed

Humans host an intestinal population of microbes-collectively referred to as the gut microbiome-which encode the carbohydrate active enzymes, or CAZymes, that are absent from the human genome. These CAZymes help to extract energy from recalcitrant polysaccharides. The question then arises as to if and how the microbiome adapts to new carbohydrate sources when modern humans change eating habits. Recent metagenome analysis of microbiomes from healthy American, Japanese, and Spanish populations identified putative CAZymes obtained by horizontal gene transfer from marine bacteria, which suggested that human gut bacteria evolved to degrade algal carbohydrates-for example, consumed in form of sushi. We approached this hypothesis by studying such a polysaccharide utilization locus (PUL) obtained by horizontal gene transfer by the gut bacterium Bacteroides plebeius. Transcriptomic and growth experiments revealed that the PUL responds to the polysaccharide porphyran from red algae, enabling growth on this carbohydrate but not related substrates like agarose and carrageenan. The X-ray crystallographic and biochemical analysis of two proteins encoded by this PUL, BACPLE_01689 and BACPLE_01693, showed that they are beta-porphyranases belonging to glycoside hydrolase families 16 and 86, respectively. The product complex of the GH86 at 1.3 A resolution highlights the molecular details of porphyran hydrolysis by this new porphyranase. Combined, these data establish experimental support for the argument that CAZymes and associated genes obtained from extrinsic microbes add new catabolic functions to the human gut microbiome.

Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes.,Hehemann JH, Kelly AG, Pudlo NA, Martens EC, Boraston AB Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19786-91. doi:, 10.1073/pnas.1211002109. Epub 2012 Nov 12. PMID:23150581^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hehemann JH, Kelly AG, Pudlo NA, Martens EC, Boraston AB. Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes. Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19786-91. doi:, 10.1073/pnas.1211002109. Epub 2012 Nov 12. PMID:23150581 doi:http://dx.doi.org/10.1073/pnas.1211002109
↑ Hehemann JH, Kelly AG, Pudlo NA, Martens EC, Boraston AB. Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes. Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19786-91. doi:, 10.1073/pnas.1211002109. Epub 2012 Nov 12. PMID:23150581 doi:http://dx.doi.org/10.1073/pnas.1211002109

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4awd"

@@ Line 3: / Line 3: @@
 <StructureSection load='4awd' size='340' side='right'caption='[[4awd]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4awd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_plebeius Bacteroides plebeius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AWD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4AWD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4awd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_plebeius Bacteroides plebeius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AWD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AWD FirstGlance]. <br>
 </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=GOL:GLYCEROL'>GOL</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-porphyranase Beta-porphyranase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.178 3.2.1.178] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-porphyranase Beta-porphyranase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.178 3.2.1.178] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=4awd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4awd OCA], [http://pdbe.org/4awd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4awd RCSB], [http://www.ebi.ac.uk/pdbsum/4awd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4awd 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=4awd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4awd OCA], [https://pdbe.org/4awd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4awd RCSB], [https://www.ebi.ac.uk/pdbsum/4awd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4awd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PORB_BACPM PORB_BACPM]] Cleaves the sulfated polysaccharide porphyran at the (1->4) linkages between beta-D-galactopyranose and alpha-L-galactopyranose-6-sulfate, forming mostly the disaccharide alpha-L-galactopyranose-6-sulfate-(1->3)-beta-D-galactose. Some longer oligosaccharides of even number of residues are also observed. Inactive on the non-sulfated agarose portion of the porphyran backbone.<ref>PMID:23150581</ref>
+[[https://www.uniprot.org/uniprot/PORB_BACPM PORB_BACPM]] Cleaves the sulfated polysaccharide porphyran at the (1->4) linkages between beta-D-galactopyranose and alpha-L-galactopyranose-6-sulfate, forming mostly the disaccharide alpha-L-galactopyranose-6-sulfate-(1->3)-beta-D-galactose. Some longer oligosaccharides of even number of residues are also observed. Inactive on the non-sulfated agarose portion of the porphyran backbone.<ref>PMID:23150581</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==

4awd

From Proteopedia

Revision as of 05:48, 25 August 2022

Crystal structure of the beta-porphyranase BpGH16B (BACPLE_01689) from the human gut bacterium Bacteroides plebeius

Structural highlights

Function

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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