|
|
| (One intermediate revision not shown.) |
| Line 3: |
Line 3: |
| | <StructureSection load='1h41' size='340' side='right'caption='[[1h41]], [[Resolution|resolution]] 1.50Å' scene=''> | | <StructureSection load='1h41' size='340' side='right'caption='[[1h41]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1h41]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"cellvibrio_cellulosa"_nagy_et_al._2002 "cellvibrio cellulosa" nagy et al. 2002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H41 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H41 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1h41]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H41 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H41 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GCV:4-O-METHYL-ALPHA-D-GLUCURONIC+ACID'>GCV</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]] 1.5Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gqi|1gqi]], [[1gqj|1gqj]], [[1gqk|1gqk]], [[1gql|1gql]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GCV:4-O-METHYL-ALPHA-D-GLUCURONIC+ACID'>GCV</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-glucuronidase Alpha-glucuronidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.139 3.2.1.139] </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=1h41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h41 OCA], [https://pdbe.org/1h41 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h41 RCSB], [https://www.ebi.ac.uk/pdbsum/1h41 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h41 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=1h41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h41 OCA], [http://pdbe.org/1h41 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1h41 RCSB], [http://www.ebi.ac.uk/pdbsum/1h41 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1h41 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/AGUA_CELJU AGUA_CELJU]] Alpha-glucuronidase involved in the hydrolysis of xylan, a major structural heterogeneous polysaccharide found in plant biomass representing the second most abundant polysaccharide in the biosphere, after cellulose. It catalyzes the cleavage of the alpha-1,2-glycosidic bond at the non-reducing end of 4-O-methyl-D-glucuronic acid (4-O-MeGlcA) side chain of short xylooligosaccharides and releases 4-O-methylglucuronic acid. It can also hydrolyze small soluble oligosaccharides such as dobiouronic acid, aldotriouronic acid, aldotetraouronic acid, and aldopentaouronic acid.<ref>PMID:11937059</ref> <ref>PMID:12169619</ref> <ref>PMID:12654910</ref> | + | [https://www.uniprot.org/uniprot/AGUA_CELJU AGUA_CELJU] Alpha-glucuronidase involved in the hydrolysis of xylan, a major structural heterogeneous polysaccharide found in plant biomass representing the second most abundant polysaccharide in the biosphere, after cellulose. It catalyzes the cleavage of the alpha-1,2-glycosidic bond at the non-reducing end of 4-O-methyl-D-glucuronic acid (4-O-MeGlcA) side chain of short xylooligosaccharides and releases 4-O-methylglucuronic acid. It can also hydrolyze small soluble oligosaccharides such as dobiouronic acid, aldotriouronic acid, aldotetraouronic acid, and aldopentaouronic acid.<ref>PMID:11937059</ref> <ref>PMID:12169619</ref> <ref>PMID:12654910</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 37: |
Line 36: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cellvibrio cellulosa nagy et al. 2002]] | + | [[Category: Cellvibrio japonicus]] |
| - | [[Category: Alpha-glucuronidase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Davies, G J]] | + | [[Category: Davies GJ]] |
| - | [[Category: Gilbert, H J]] | + | [[Category: Gilbert HJ]] |
| - | [[Category: Nagy, T]] | + | [[Category: Nagy T]] |
| - | [[Category: Nurizzo, D]] | + | [[Category: Nurizzo D]] |
| - | [[Category: Glucuronic acid]]
| + | |
| - | [[Category: Glucuronidase]]
| + | |
| - | [[Category: Glycoside hydrolase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
AGUA_CELJU Alpha-glucuronidase involved in the hydrolysis of xylan, a major structural heterogeneous polysaccharide found in plant biomass representing the second most abundant polysaccharide in the biosphere, after cellulose. It catalyzes the cleavage of the alpha-1,2-glycosidic bond at the non-reducing end of 4-O-methyl-D-glucuronic acid (4-O-MeGlcA) side chain of short xylooligosaccharides and releases 4-O-methylglucuronic acid. It can also hydrolyze small soluble oligosaccharides such as dobiouronic acid, aldotriouronic acid, aldotetraouronic acid, and aldopentaouronic acid.[1] [2] [3]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
alpha-Glucuronidases are key components of the ensemble of enzymes that degrade the plant cell wall. They hydrolyze the alpha1,2-glycosidic bond between 4-O-methyl-d-glucuronic acid (4-O-MeGlcA) and the xylan or xylooligosaccharide backbone. Here we report the crystal structure of an inactive mutant (E292A) of the alpha-glucuronidase, GlcA67A, from Cellvibrio japonicus in complex with its substrate. The data show that the 4-O-methyl group of the substrate is accommodated within a hydrophobic sheath flanked by Val-210 and Trp-160, whereas the carboxylate moiety is located within a positively charged region of the substrate-binding pocket. The carboxylate side chains of Glu-393 and Asp-365, on the "beta-face" of 4-O-MeGlcA, form hydrogen bonds with a water molecule that is perfectly positioned to mount a nucleophilic attack at the anomeric carbon of the target glycosidic bond, providing further support for the view that, singly or together, these amino acids function as the catalytic base. The capacity of reaction products and product analogues to inhibit GlcA67A shows that the 4-O-methyl group, the carboxylate, and the xylose sugar of aldobiouronic acid all play an important role in substrate binding. Site-directed mutagenesis informed by the crystal structure of enzyme-ligand complexes was used to probe the importance of highly conserved residues at the active site of GlcA67A. The biochemical properties of K288A, R325A, and K360A show that a constellation of three basic amino acids (Lys-288, Arg-325, and Lys-360) plays a critical role in binding the carboxylate moiety of 4-O-MeGlcA. Disruption of the apolar nature of the pocket created by Val-210 (V210N and V210S) has a detrimental effect on substrate binding, although the reduction in affinity is not reflected by an inability to accommodate the 4-O-methyl group. Replacing the two tryptophan residues that stack against the sugar rings of the substrate with alanine (W160A and W543A) greatly reduced activity.
The alpha-glucuronidase, GlcA67A, of Cellvibrio japonicus utilizes the carboxylate and methyl groups of aldobiouronic acid as important substrate recognition determinants.,Nagy T, Nurizzo D, Davies GJ, Biely P, Lakey JH, Bolam DN, Gilbert HJ J Biol Chem. 2003 May 30;278(22):20286-92. Epub 2003 Mar 24. PMID:12654910[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Nurizzo D, Nagy T, Gilbert HJ, Davies GJ. The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A. Structure. 2002 Apr;10(4):547-56. PMID:11937059
- ↑ Nagy T, Emami K, Fontes CM, Ferreira LM, Humphry DR, Gilbert HJ. The membrane-bound alpha-glucuronidase from Pseudomonas cellulosa hydrolyzes 4-O-methyl-D-glucuronoxylooligosaccharides but not 4-O-methyl-D-glucuronoxylan. J Bacteriol. 2002 Sep;184(17):4925-9. PMID:12169619
- ↑ Nagy T, Nurizzo D, Davies GJ, Biely P, Lakey JH, Bolam DN, Gilbert HJ. The alpha-glucuronidase, GlcA67A, of Cellvibrio japonicus utilizes the carboxylate and methyl groups of aldobiouronic acid as important substrate recognition determinants. J Biol Chem. 2003 May 30;278(22):20286-92. Epub 2003 Mar 24. PMID:12654910 doi:10.1074/jbc.M302205200
- ↑ Nagy T, Nurizzo D, Davies GJ, Biely P, Lakey JH, Bolam DN, Gilbert HJ. The alpha-glucuronidase, GlcA67A, of Cellvibrio japonicus utilizes the carboxylate and methyl groups of aldobiouronic acid as important substrate recognition determinants. J Biol Chem. 2003 May 30;278(22):20286-92. Epub 2003 Mar 24. PMID:12654910 doi:10.1074/jbc.M302205200
|
