3gnp

From Proteopedia

(Difference between revisions)

Revision as of 22:47, 9 February 2016

Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with Octyl-Beta-D-Thio-Glucoside

Structural highlights

3gnp is a 1 chain structure with sequence from Japanese rice. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	3gno, 3gnr
Gene:	LOC_Os03g11420, Os03g0212800, Os3bglu6 locus ID: Os03g0212800 (Japanese rice)
Activity:	Beta-glucosidase, with EC number 3.2.1.21
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[BGL06_ORYSJ] Hydrolyzes glycosides, oligosaccharides and hydrophobic glycosides.

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

Glycoside hydrolase family 1 (GH1) beta-glucosidases play roles in many processes in plants, such as chemical defense, alkaloid metabolism, hydrolysis of cell wall-derived oligosaccharides, phytohormone regulation, and lignification. However, the functions of most of the 34 GH1 gene products in rice (Oryza sativa) are unknown. Os3BGlu6, a rice beta-glucosidase representing a previously uncharacterized phylogenetic cluster of GH1, was produced in recombinant Escherichia coli. Os3BGlu6 hydrolyzed p-nitrophenyl (pNP)-beta-d-fucoside (k(cat)/K(m) = 67 mm(-1) s(-1)), pNP-beta-d-glucoside (k(cat)/K(m) = 6.2 mm(-1) s(-1)), and pNP-beta-d-galactoside (k(cat)/K(m) = 1.6 mm(-1)s(-1)) efficiently but had little activity toward other pNP glycosides. It also had high activity toward n-octyl-beta-d-glucoside and beta-(1-->3)- and beta-(1-->2)-linked disaccharides and was able to hydrolyze apigenin beta-glucoside and several other natural glycosides. Crystal structures of Os3BGlu6 and its complexes with a covalent intermediate, 2-deoxy-2-fluoroglucoside, and a nonhydrolyzable substrate analog, n-octyl-beta-d-thioglucopyranoside, were solved at 1.83, 1.81, and 1.80 A resolution, respectively. The position of the covalently trapped 2-F-glucosyl residue in the enzyme was similar to that in a 2-F-glucosyl intermediate complex of Os3BGlu7 (rice BGlu1). The side chain of methionine-251 in the mouth of the active site appeared to block the binding of extended beta-(1-->4)-linked oligosaccharides and interact with the hydrophobic aglycone of n-octyl-beta-d-thioglucopyranoside. This correlates with the preference of Os3BGlu6 for short oligosaccharides and hydrophobic glycosides.

Structural and enzymatic characterization of Os3BGlu6, a rice beta-glucosidase hydrolyzing hydrophobic glycosides and (1->3)- and (1->2)-linked disaccharides.,Seshadri S, Akiyama T, Opassiri R, Kuaprasert B, Cairns JK Plant Physiol. 2009 Sep;151(1):47-58. Epub 2009 Jul 8. PMID:19587102^[1]

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

References

↑ Seshadri S, Akiyama T, Opassiri R, Kuaprasert B, Cairns JK. Structural and enzymatic characterization of Os3BGlu6, a rice beta-glucosidase hydrolyzing hydrophobic glycosides and (1->3)- and (1->2)-linked disaccharides. Plant Physiol. 2009 Sep;151(1):47-58. Epub 2009 Jul 8. PMID:19587102 doi:10.1104/pp.109.139436

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3gnp"

@@ Line 2: / Line 2: @@
 <StructureSection load='3gnp' size='340' side='right' caption='[[3gnp]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3gnp]] is a 1 chain structure with 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=3GNP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GNP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3gnp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GNP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GNP FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SOG:2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL'>SOG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gno|3gno]], [[3gnr|3gnr]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LOC_Os03g11420, Os03g0212800, Os3bglu6 locus ID: Os03g0212800 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Oryza sativa Japonica Group])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LOC_Os03g11420, Os03g0212800, Os3bglu6 locus ID: Os03g0212800 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></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=3gnp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gnp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gnp RCSB], [http://www.ebi.ac.uk/pdbsum/3gnp PDBsum]</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=3gnp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gnp OCA], [http://pdbe.org/3gnp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gnp RCSB], [http://www.ebi.ac.uk/pdbsum/3gnp PDBsum]</span></td></tr>
 </table>
+== Function ==
+[[http://www.uniprot.org/uniprot/BGL06_ORYSJ BGL06_ORYSJ]] Hydrolyzes glycosides, oligosaccharides and hydrophobic glycosides.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 19: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3gnp ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3gnp" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 35: / Line 38: @@
 </StructureSection>
 [[Category: Beta-glucosidase]]
-[[Category: Oryza sativa japonica group]]
+[[Category: Japanese rice]]
 [[Category: Akiyama, T]]
 [[Category: Cairns, J R.K]]

3gnp

From Proteopedia

Revision as of 22:47, 9 February 2016

Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with Octyl-Beta-D-Thio-Glucoside

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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