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| | <StructureSection load='1vd5' size='340' side='right'caption='[[1vd5]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='1vd5' size='340' side='right'caption='[[1vd5]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1vd5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacgl Bacgl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VD5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1vd5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._GL1 Bacillus sp. GL1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VD5 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 1.8Å</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=1vd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vd5 OCA], [https://pdbe.org/1vd5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vd5 RCSB], [https://www.ebi.ac.uk/pdbsum/1vd5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vd5 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=1vd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vd5 OCA], [https://pdbe.org/1vd5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vd5 RCSB], [https://www.ebi.ac.uk/pdbsum/1vd5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vd5 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/UGL_BACGL UGL_BACGL]] Catalyzes the hydrolysis of oligosaccharides with unsaturated glucuronyl residues at the non-reducing terminal, to a sugar or an amino sugar, and an unsaturated D-glucuronic acid (GlcA), which is nonenzymatically converted immediately to alpha-keto acid.<ref>PMID:10441389</ref> <ref>PMID:21147778</ref>
| + | [https://www.uniprot.org/uniprot/UGL_BACGL UGL_BACGL] Catalyzes the hydrolysis of oligosaccharides with unsaturated glucuronyl residues at the non-reducing terminal, to a sugar or an amino sugar, and an unsaturated D-glucuronic acid (GlcA), which is nonenzymatically converted immediately to alpha-keto acid.<ref>PMID:10441389</ref> <ref>PMID:21147778</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacgl]] | + | [[Category: Bacillus sp. GL1]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Akao, S]] | + | [[Category: Akao S]] |
| - | [[Category: Hashimoto, W]] | + | [[Category: Hashimoto W]] |
| - | [[Category: Itoh, T]] | + | [[Category: Itoh T]] |
| - | [[Category: Mikami, B]] | + | [[Category: Mikami B]] |
| - | [[Category: Murata, K]] | + | [[Category: Murata K]] |
| - | [[Category: Alpha-alpha-barrel]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Unsaturated glucuronyl hydrolase]]
| + | |
| Structural highlights
Function
UGL_BACGL Catalyzes the hydrolysis of oligosaccharides with unsaturated glucuronyl residues at the non-reducing terminal, to a sugar or an amino sugar, and an unsaturated D-glucuronic acid (GlcA), which is nonenzymatically converted immediately to alpha-keto acid.[1] [2]
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
Unsaturated glucuronyl hydrolase (UGL) is a novel glycosaminoglycan hydrolase that releases unsaturated d-glucuronic acid from oligosaccharides produced by polysaccharide lyases. The x-ray crystallographic structure of UGL from Bacillus sp. GL1 was first determined by multiple isomorphous replacement (mir) and refined at 1.8 A resolution with a final R-factor of 16.8% for 25 to 1.8 A resolution data. The refined UGL structure consists of 377 amino acid residues and 478 water molecules, four glycine molecules, two dithiothreitol (DTT) molecules, and one 2-methyl-2,4-pentanediol (MPD) molecule. UGL includes an alpha(6)/alpha(6)-barrel, whose structure is found in the six-hairpin enzyme superfamily of an alpha/alpha-toroidal fold. One side of the UGL alpha(6)/alpha(6)-barrel structure consists of long loops containing three short beta-sheets and contributes to the formation of a deep pocket. One glycine molecule and two DTT molecules surrounded by highly conserved amino acid residues in UGLs were found in the pocket, suggesting that catalytic and substrate-binding sites are located in this pocket. The overall UGL structure, with the exception of some loops, very much resembled that of the Bacillus subtilis hypothetical protein Yter, whose function is unknown and which exhibits little amino acid sequence identity with UGL. In the active pocket, residues possibly involved in substrate recognition and catalysis by UGL are conserved in UGLs and Yter. The most likely candidate catalytic residues for glycosyl hydrolysis are Asp(88) and Asp(149). This was supported by site-directed mutagenesis studies in Asp(88) and Asp(149).
Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution.,Itoh T, Akao S, Hashimoto W, Mikami B, Murata K J Biol Chem. 2004 Jul 23;279(30):31804-12. Epub 2004 May 17. PMID:15148314[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Hashimoto W, Kobayashi E, Nankai H, Sato N, Miya T, Kawai S, Murata K. Unsaturated glucuronyl hydrolase of Bacillus sp. GL1: novel enzyme prerequisite for metabolism of unsaturated oligosaccharides produced by polysaccharide lyases. Arch Biochem Biophys. 1999 Aug 15;368(2):367-74. PMID:10441389 doi:http://dx.doi.org/10.1006/abbi.1999.1305
- ↑ Nakamichi Y, Maruyama Y, Mikami B, Hashimoto W, Murata K. Structural determinants in streptococcal unsaturated glucuronyl hydrolase for recognition of glycosaminoglycan sulfate groups. J Biol Chem. 2011 Feb 25;286(8):6262-71. Epub 2010 Dec 8. PMID:21147778 doi:10.1074/jbc.M110.182618
- ↑ Itoh T, Akao S, Hashimoto W, Mikami B, Murata K. Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution. J Biol Chem. 2004 Jul 23;279(30):31804-12. Epub 2004 May 17. PMID:15148314 doi:10.1074/jbc.M403288200
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