2rgl
From Proteopedia
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|PDB= 2rgl |SIZE=350|CAPTION= <scene name='initialview01'>2rgl</scene>, resolution 2.20Å | |PDB= 2rgl |SIZE=350|CAPTION= <scene name='initialview01'>2rgl</scene>, resolution 2.20Å | ||
|SITE= <scene name='pdbsite=AC1:Zn+Binding+Site+For+Residue+A+1001'>AC1</scene>, <scene name='pdbsite=AC2:So4+Binding+Site+For+Residue+A+1002'>AC2</scene>, <scene name='pdbsite=AC3:So4+Binding+Site+For+Residue+B+1002'>AC3</scene>, <scene name='pdbsite=AC4:Mes+Binding+Site+For+Residue+A+1003'>AC4</scene>, <scene name='pdbsite=AC5:Mes+Binding+Site+For+Residue+B+1003'>AC5</scene>, <scene name='pdbsite=AC6:Gol+Binding+Site+For+Residue+A+1004'>AC6</scene> and <scene name='pdbsite=AC7:Gol+Binding+Site+For+Residue+B+1004'>AC7</scene> | |SITE= <scene name='pdbsite=AC1:Zn+Binding+Site+For+Residue+A+1001'>AC1</scene>, <scene name='pdbsite=AC2:So4+Binding+Site+For+Residue+A+1002'>AC2</scene>, <scene name='pdbsite=AC3:So4+Binding+Site+For+Residue+B+1002'>AC3</scene>, <scene name='pdbsite=AC4:Mes+Binding+Site+For+Residue+A+1003'>AC4</scene>, <scene name='pdbsite=AC5:Mes+Binding+Site+For+Residue+B+1003'>AC5</scene>, <scene name='pdbsite=AC6:Gol+Binding+Site+For+Residue+A+1004'>AC6</scene> and <scene name='pdbsite=AC7:Gol+Binding+Site+For+Residue+B+1004'>AC7</scene> | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] </span> |
|GENE= Os3bglu7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Oryza sativa Japonica Group]) | |GENE= Os3bglu7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Oryza sativa Japonica Group]) | ||
| + | |DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00232 Glyco_hydro_1]</span> | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgl OCA], [http://www.ebi.ac.uk/pdbsum/2rgl PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2rgl RCSB]</span> | ||
}} | }} | ||
'''Rice BGlu1 beta-glucosidase, a plant exoglucanase/beta-glucosidase''' | '''Rice BGlu1 beta-glucosidase, a plant exoglucanase/beta-glucosidase''' | ||
| + | |||
| + | ==Overview== | ||
| + | The structures of rice BGlu1 beta-glucosidase, a plant beta-glucosidase active in hydrolyzing cell wall-derived oligosaccharides, and its covalent intermediate with 2-deoxy-2-fluoroglucoside have been solved at 2.2 A and 1.55 A resolution, respectively. The structures were similar to the known structures of other glycosyl hydrolase family 1 (GH1) beta-glucosidases, but showed several differences in the loops around the active site, which lead to an open active site with a narrow slot at the bottom, compatible with the hydrolysis of long beta-1,4-linked oligosaccharides. Though this active site structure is somewhat similar to that of the Paenibacillus polymyxa beta-glucosidase B, which hydrolyzes similar oligosaccharides, molecular docking studies indicate that the residues interacting with the substrate beyond the conserved -1 site are completely different, reflecting the independent evolution of plant and microbial GH1 exo-beta-glucanase/beta-glucosidases. The complex with the 2-fluoroglucoside included a glycerol molecule, which appears to be in a position to make a nucleophilic attack on the anomeric carbon in a transglycosylation reaction. The coordination of the hydroxyl groups suggests that sugars are positioned as acceptors for transglycosylation by their interactions with E176, the catalytic acid/base, and Y131, which is conserved in barley BGQ60/beta-II beta-glucosidase, that has oligosaccharide hydrolysis and transglycosylation activity similar to rice BGlu1. As the rice and barley enzymes have different preferences for cellobiose and cellotriose, residues that appeared to interact with docked oligosaccharides were mutated to those of the barley enzyme to see if the relative activities of rice BGlu1 toward these substrates could be changed to those of BGQ60. Although no single residue appeared to be responsible for these differences, I179, N190 and N245 did appear to interact with the substrates. | ||
==About this Structure== | ==About this Structure== | ||
2RGL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Oryza_sativa_japonica_group Oryza sativa japonica group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RGL OCA]. | 2RGL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Oryza_sativa_japonica_group Oryza sativa japonica group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RGL OCA]. | ||
| + | |||
| + | ==Reference== | ||
| + | Structural insights into rice BGlu1 beta-glucosidase oligosaccharide hydrolysis and transglycosylation., Chuenchor W, Pengthaisong S, Robinson RC, Yuvaniyama J, Oonanant W, Bevan DR, Esen A, Chen CJ, Opassiri R, Svasti J, Cairns JR, J Mol Biol. 2008 Apr 4;377(4):1200-15. Epub 2008 Feb 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18308333 18308333] | ||
[[Category: Beta-glucosidase]] | [[Category: Beta-glucosidase]] | ||
[[Category: Oryza sativa japonica group]] | [[Category: Oryza sativa japonica group]] | ||
| Line 23: | Line 31: | ||
[[Category: Robinson, R C.]] | [[Category: Robinson, R C.]] | ||
[[Category: Yuvaniyama, J.]] | [[Category: Yuvaniyama, J.]] | ||
| - | [[Category: GOL]] | ||
| - | [[Category: MES]] | ||
| - | [[Category: SO4]] | ||
| - | [[Category: ZN]] | ||
[[Category: beta-alpha-barrel]] | [[Category: beta-alpha-barrel]] | ||
[[Category: glycosidase]] | [[Category: glycosidase]] | ||
[[Category: hydrolase]] | [[Category: hydrolase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 10:02:49 2008'' |
Revision as of 08:02, 26 March 2008
| |||||||
| , resolution 2.20Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , , , and | ||||||
| Ligands: | , , , | ||||||
| Gene: | Os3bglu7 (Oryza sativa Japonica Group) | ||||||
| Activity: | Beta-glucosidase, with EC number 3.2.1.21 | ||||||
| Domains: | Glyco_hydro_1 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, JenaLib, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Rice BGlu1 beta-glucosidase, a plant exoglucanase/beta-glucosidase
Overview
The structures of rice BGlu1 beta-glucosidase, a plant beta-glucosidase active in hydrolyzing cell wall-derived oligosaccharides, and its covalent intermediate with 2-deoxy-2-fluoroglucoside have been solved at 2.2 A and 1.55 A resolution, respectively. The structures were similar to the known structures of other glycosyl hydrolase family 1 (GH1) beta-glucosidases, but showed several differences in the loops around the active site, which lead to an open active site with a narrow slot at the bottom, compatible with the hydrolysis of long beta-1,4-linked oligosaccharides. Though this active site structure is somewhat similar to that of the Paenibacillus polymyxa beta-glucosidase B, which hydrolyzes similar oligosaccharides, molecular docking studies indicate that the residues interacting with the substrate beyond the conserved -1 site are completely different, reflecting the independent evolution of plant and microbial GH1 exo-beta-glucanase/beta-glucosidases. The complex with the 2-fluoroglucoside included a glycerol molecule, which appears to be in a position to make a nucleophilic attack on the anomeric carbon in a transglycosylation reaction. The coordination of the hydroxyl groups suggests that sugars are positioned as acceptors for transglycosylation by their interactions with E176, the catalytic acid/base, and Y131, which is conserved in barley BGQ60/beta-II beta-glucosidase, that has oligosaccharide hydrolysis and transglycosylation activity similar to rice BGlu1. As the rice and barley enzymes have different preferences for cellobiose and cellotriose, residues that appeared to interact with docked oligosaccharides were mutated to those of the barley enzyme to see if the relative activities of rice BGlu1 toward these substrates could be changed to those of BGQ60. Although no single residue appeared to be responsible for these differences, I179, N190 and N245 did appear to interact with the substrates.
About this Structure
2RGL is a Single protein structure of sequence from Oryza sativa japonica group. Full crystallographic information is available from OCA.
Reference
Structural insights into rice BGlu1 beta-glucosidase oligosaccharide hydrolysis and transglycosylation., Chuenchor W, Pengthaisong S, Robinson RC, Yuvaniyama J, Oonanant W, Bevan DR, Esen A, Chen CJ, Opassiri R, Svasti J, Cairns JR, J Mol Biol. 2008 Apr 4;377(4):1200-15. Epub 2008 Feb 4. PMID:18308333
Page seeded by OCA on Wed Mar 26 10:02:49 2008
