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5by3

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A novel family GH115 4-O-Methyl-alpha-glucuronidase, BtGH115A, with specificity for decorated arabinogalactans

Structural highlights

5by3 is a 1 chain structure with sequence from Bacteroides thetaiotaomicron VPI-5482. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q8A3J6_BACTN

Publication Abstract from PubMed

Glycoside hydrolases are clustered into families based on amino acid sequence similarities, and belonging to a particular family can infer biological activity of an enzyme. Family GH115 contains alpha-glucuronidases where several members have been shown to hydrolyze terminal alpha-1,2-linked glucuronic acid and 4-O-methylated glucuronic acid from the plant cell wall polysaccharide glucuronoxylan. Other GH115 enzymes show no activity on glucuronoxylan, and therefore, it has been proposed that family GH115 may be a poly-specific family. In this study, we reveal that a putative periplasmic GH115 from the human gut symbiont Bacteroides thetaiotaomicron, BtGH115A, hydrolyzes terminal 4-O-methyl-glucuronic acid residues from decorated arabinogalactan isolated from acacia tree. The three-dimensional structure of BtGH115A reveals that BtGH115A has the same domain architecture as the other structurally characterized member of this family, BoAgu115A; however the position of the C-terminal module is altered with respect to each individual enzyme. Phylogenetic analysis of GH115 amino sequences divides the family into distinct clades that may distinguish different substrate specificities. Finally, we show that BtGH115A alpha-glucuronidase activity is necessary for the sequential digestion of branched galactans from acacia gum by a galactan-beta-1,3-galactosidase from family GH43; however, while B. thetaiotaomicron grows on larch wood arabinogalactan, the bacterium is not able to metabolize acacia gum arabinogalactan, suggesting that BtGH115A is involved in degradation of arabinogalactan fragments liberated by other microbial species in the gastrointestinal tract.

Structural and Functional Characterization of a Novel Family GH115 4-O-Methyl-alpha-Glucuronidase with Specificity for Decorated Arabinogalactans.,Aalbers F, Turkenburg JP, Davies GJ, Dijkhuizen L, Lammerts van Bueren A J Mol Biol. 2015 Jul 14. pii: S0022-2836(15)00384-8. doi:, 10.1016/j.jmb.2015.07.006. PMID:26186997^[1]

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

References

↑ Aalbers F, Turkenburg JP, Davies GJ, Dijkhuizen L, Lammerts van Bueren A. Structural and Functional Characterization of a Novel Family GH115 4-O-Methyl-alpha-Glucuronidase with Specificity for Decorated Arabinogalactans. J Mol Biol. 2015 Jul 14. pii: S0022-2836(15)00384-8. doi:, 10.1016/j.jmb.2015.07.006. PMID:26186997 doi:http://dx.doi.org/10.1016/j.jmb.2015.07.006

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/5by3"

Categories: Bacteroides thetaiotaomicron VPI-5482 | Large Structures | Davies GJ | Lammerts van Bueren A | Turkenburg JP

@@ Line 3: / Line 3: @@
 <StructureSection load='5by3' size='340' side='right'caption='[[5by3]], [[Resolution|resolution]] 2.44&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5by3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BY3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BY3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5by3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BY3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BY3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=5by3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5by3 OCA], [https://pdbe.org/5by3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5by3 RCSB], [https://www.ebi.ac.uk/pdbsum/5by3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5by3 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BT_2958 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5by3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5by3 OCA], [http://pdbe.org/5by3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5by3 RCSB], [http://www.ebi.ac.uk/pdbsum/5by3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5by3 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8A3J6_BACTN Q8A3J6_BACTN]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Bactn]]
+[[Category: Bacteroides thetaiotaomicron VPI-5482]]
 [[Category: Large Structures]]
-[[Category: Bueren, A Lammerts van]]
+[[Category: Davies GJ]]
-[[Category: Davies, G J]]
+[[Category: Lammerts van Bueren A]]
-[[Category: Turkenburg, J P]]
+[[Category: Turkenburg JP]]
-[[Category: Arabinogalactans alpha-glucuronidase]]
-[[Category: Glycoside]]
-[[Category: Hydrolase]]
-[[Category: Sugar binding protein]]

5by3

From Proteopedia

Current revision

A novel family GH115 4-O-Methyl-alpha-glucuronidase, BtGH115A, with specificity for decorated arabinogalactans

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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