6hpd

From Proteopedia

(Difference between revisions)

Current revision

The structure of a beta-glucuronidase from glycoside hydrolase family 2

Structural highlights

6hpd is a 1 chain structure with sequence from Formosa agariphila KMM 3901. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.43Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PLH17_FORAG Beta-glucuronidase involved in ulvan degradation (PubMed:31285597). Ulvan is the main polysaccharide component of the Ulvales (green seaweed) cell wall. It is composed of disaccharide building blocks comprising 3-sulfated rhamnose (Rha3S) linked to D-glucuronic acid (GlcA), L-iduronic acid (IduA), or D-xylose (Xyl) (Probable). Beta-glucuronidase removes GlcA side chains present on some O2 residues of Rha3S. Can remove the GlcA side chains from polymeric ulvan or from smaller oligomers (PubMed:31285597).^[1] ^[2]

Publication Abstract from PubMed

Marine seaweeds increasingly grow into extensive algal blooms, which are detrimental to coastal ecosystems, tourism and aquaculture. However, algal biomass is also emerging as a sustainable raw material for the bioeconomy. The potential exploitation of algae is hindered by our limited knowledge of the microbial pathways-and hence the distinct biochemical functions of the enzymes involved-that convert algal polysaccharides into oligo- and monosaccharides. Understanding these processes would be essential, however, for applications such as the fermentation of algal biomass into bioethanol or other value-added compounds. Here, we describe the metabolic pathway that enables the marine flavobacterium Formosa agariphila to degrade ulvan, the main cell wall polysaccharide of bloom-forming Ulva species. The pathway involves 12 biochemically characterized carbohydrate-active enzymes, including two polysaccharide lyases, three sulfatases and seven glycoside hydrolases that sequentially break down ulvan into fermentable monosaccharides. This way, the enzymes turn a previously unexploited renewable into a valuable and ecologically sustainable bioresource.

A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan.,Reisky L, Prechoux A, Zuhlke MK, Baumgen M, Robb CS, Gerlach N, Roret T, Stanetty C, Larocque R, Michel G, Song T, Markert S, Unfried F, Mihovilovic MD, Trautwein-Schult A, Becher D, Schweder T, Bornscheuer UT, Hehemann JH Nat Chem Biol. 2019 Jul 8. pii: 10.1038/s41589-019-0311-9. doi:, 10.1038/s41589-019-0311-9. PMID:31285597^[3]

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

References

↑ Reisky L, Prechoux A, Zuhlke MK, Baumgen M, Robb CS, Gerlach N, Roret T, Stanetty C, Larocque R, Michel G, Song T, Markert S, Unfried F, Mihovilovic MD, Trautwein-Schult A, Becher D, Schweder T, Bornscheuer UT, Hehemann JH. A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Nat Chem Biol. 2019 Jul 8. pii: 10.1038/s41589-019-0311-9. doi:, 10.1038/s41589-019-0311-9. PMID:31285597 doi:http://dx.doi.org/10.1038/s41589-019-0311-9
↑ Reisky L, Prechoux A, Zuhlke MK, Baumgen M, Robb CS, Gerlach N, Roret T, Stanetty C, Larocque R, Michel G, Song T, Markert S, Unfried F, Mihovilovic MD, Trautwein-Schult A, Becher D, Schweder T, Bornscheuer UT, Hehemann JH. A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Nat Chem Biol. 2019 Jul 8. pii: 10.1038/s41589-019-0311-9. doi:, 10.1038/s41589-019-0311-9. PMID:31285597 doi:http://dx.doi.org/10.1038/s41589-019-0311-9
↑ Reisky L, Prechoux A, Zuhlke MK, Baumgen M, Robb CS, Gerlach N, Roret T, Stanetty C, Larocque R, Michel G, Song T, Markert S, Unfried F, Mihovilovic MD, Trautwein-Schult A, Becher D, Schweder T, Bornscheuer UT, Hehemann JH. A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Nat Chem Biol. 2019 Jul 8. pii: 10.1038/s41589-019-0311-9. doi:, 10.1038/s41589-019-0311-9. PMID:31285597 doi:http://dx.doi.org/10.1038/s41589-019-0311-9

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6hpd"

@@ Line 3: / Line 3: @@
 <StructureSection load='6hpd' size='340' side='right'caption='[[6hpd]], [[Resolution|resolution]] 2.43&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6hpd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroidetes_bacterium_kmm_3901 Bacteroidetes bacterium kmm 3901]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HPD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6hpd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Formosa_agariphila_KMM_3901 Formosa agariphila KMM 3901]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HPD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.43&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BN863_22060 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1347342 Bacteroidetes bacterium KMM 3901])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </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=6hpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hpd OCA], [https://pdbe.org/6hpd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hpd RCSB], [https://www.ebi.ac.uk/pdbsum/6hpd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hpd ProSAT]</span></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=6hpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hpd OCA], [http://pdbe.org/6hpd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hpd RCSB], [http://www.ebi.ac.uk/pdbsum/6hpd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hpd ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PLH17_FORAG PLH17_FORAG] Beta-glucuronidase involved in ulvan degradation (PubMed:31285597). Ulvan is the main polysaccharide component of the Ulvales (green seaweed) cell wall. It is composed of disaccharide building blocks comprising 3-sulfated rhamnose (Rha3S) linked to D-glucuronic acid (GlcA), L-iduronic acid (IduA), or D-xylose (Xyl) (Probable). Beta-glucuronidase removes GlcA side chains present on some O2 residues of Rha3S. Can remove the GlcA side chains from polymeric ulvan or from smaller oligomers (PubMed:31285597).<ref>PMID:31285597</ref> <ref>PMID:31285597</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 6hpd" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Galactosidase 3D structures|Galactosidase 3D structures]]
+*[[Glucuronisidase 3D structures|Glucuronisidase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacteroidetes bacterium kmm 3901]]
+[[Category: Formosa agariphila KMM 3901]]
-[[Category: Beta-galactosidase]]
 [[Category: Large Structures]]
-[[Category: Bornshoeru, U]]
+[[Category: Bornshoeru U]]
-[[Category: Gerlach, N]]
+[[Category: Gerlach N]]
-[[Category: Hehemann, J H]]
+[[Category: Hehemann JH]]
-[[Category: Reisky, L]]
+[[Category: Reisky L]]
-[[Category: Robb, C S]]
+[[Category: Robb CS]]
-[[Category: Gh2]]
-[[Category: Glucuronidase]]
-[[Category: Glycoside hydrolase]]
-[[Category: Hydrolase]]

6hpd

From Proteopedia

Current revision

The structure of a beta-glucuronidase from glycoside hydrolase family 2

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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