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[[Image:3ptm.jpg|left|200px]]


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==The crystal structure of rice (Oryza sativa L.) Os4BGlu12 with 2-fluoroglucopyranoside==
The line below this paragraph, containing "STRUCTURE_3ptm", creates the "Structure Box" on the page.
<StructureSection load='3ptm' size='340' side='right'caption='[[3ptm]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3ptm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PTM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PTM FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G2F:2-DEOXY-2-FLUORO-ALPHA-D-GLUCOPYRANOSE'>G2F</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
{{STRUCTURE_3ptm|  PDB=3ptm  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ptm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ptm OCA], [https://pdbe.org/3ptm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ptm RCSB], [https://www.ebi.ac.uk/pdbsum/3ptm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ptm ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/BGL12_ORYSI BGL12_ORYSI] Hydrolyzes p-nitrophenyl beta-D-glucoside, p-nitrophenyl beta-D-galactoside, p-nitrophenyl beta-D-xyloside, p-nitrophenyl beta-D-fucoside, p-nitrophenyl beta-L-arabinoside, cello-oligosaccharides and laminaribiose.[UniProtKB:Q7XKV4]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Rice Os4BGlu12, a glycoside hydrolase family 1 (GH1) beta-glucosidase, hydrolyzes beta-(1,4)-linked oligosaccharides of 3-6 glucosyl residues and the beta-(1,3)-linked disaccharide laminaribiose, as well as certain glycosides. The crystal structures of apo Os4BGlu12, and its complexes with 2,4-dinitrophenyl-2-deoxyl-2-fluoroglucoside (DNP2FG) and 2-deoxy-2-fluoroglucose (G2F) were solved at 2.50, 2.45 and 2.40A resolution, respectively. The overall structure of rice Os4BGlu12 is typical of GH1 enzymes, but it contains an extra disulfide bridge in the loop B region. The glucose ring of the G2F in the covalent intermediate was found in a (4)C(1) chair conformation, while that of the noncovalently bound DNP2FG had a (1)S(3) skew boat, consistent with hydrolysis via a (4)H(3) half-chair transition state. The position of the catalytic nucleophile (Glu393) in the G2F structure was more similar to that of the Sinapsis alba myrosinase G2F complex than to that in covalent intermediates of other O-glucosidases, such as rice Os3BGlu6 and Os3BGlu7 beta-glucosidases. This correlated with a significant thioglucosidase activity for Os4BGlu12, although with 200- to 1200-fold lower k(cat)/K(m) values for S-glucosides than the comparable O-glucosides, while hydrolysis of S-glucosides was undetectable for Os3BGlu6 and Os3BGlu7.


===The crystal structure of rice (Oryza sativa L.) Os4BGlu12 with 2-fluoroglucopyranoside===
The crystal structure of rice (Oryza sativa L.) Os4BGlu12, an oligosaccharide and tuberonic acid glucoside-hydrolyzing beta-glucosidase with significant thioglucohydrolase activity.,Sansenya S, Opassiri R, Kuaprasert B, Chen CJ, Ketudat Cairns JR Arch Biochem Biophys. 2011 Jun 1;510(1):62-72. Epub 2011 Apr 16. PMID:21521631<ref>PMID:21521631</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ptm" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_21521631}}, adds the Publication Abstract to the page
*[[Beta-glucosidase 3D structures|Beta-glucosidase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 21521631 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_21521631}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[3ptm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PTM OCA].
 
==Reference==
<ref group="xtra">PMID:021521631</ref><references group="xtra"/>
[[Category: Beta-glucosidase]]
[[Category: Oryza sativa]]
[[Category: Oryza sativa]]
[[Category: Cairns, J R.Ketudat.]]
[[Category: Chen CJ]]
[[Category: Chen, C J.]]
[[Category: Ketudat Cairns JR]]
[[Category: Kuaprasert, B.]]
[[Category: Kuaprasert B]]
[[Category: Opassiri, R.]]
[[Category: Opassiri R]]
[[Category: Sansenya, S.]]
[[Category: Sansenya S]]

Latest revision as of 11:06, 9 October 2024

The crystal structure of rice (Oryza sativa L.) Os4BGlu12 with 2-fluoroglucopyranosideThe crystal structure of rice (Oryza sativa L.) Os4BGlu12 with 2-fluoroglucopyranoside

Structural highlights

3ptm is a 2 chain structure with sequence from Oryza sativa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BGL12_ORYSI Hydrolyzes p-nitrophenyl beta-D-glucoside, p-nitrophenyl beta-D-galactoside, p-nitrophenyl beta-D-xyloside, p-nitrophenyl beta-D-fucoside, p-nitrophenyl beta-L-arabinoside, cello-oligosaccharides and laminaribiose.[UniProtKB:Q7XKV4]

Publication Abstract from PubMed

Rice Os4BGlu12, a glycoside hydrolase family 1 (GH1) beta-glucosidase, hydrolyzes beta-(1,4)-linked oligosaccharides of 3-6 glucosyl residues and the beta-(1,3)-linked disaccharide laminaribiose, as well as certain glycosides. The crystal structures of apo Os4BGlu12, and its complexes with 2,4-dinitrophenyl-2-deoxyl-2-fluoroglucoside (DNP2FG) and 2-deoxy-2-fluoroglucose (G2F) were solved at 2.50, 2.45 and 2.40A resolution, respectively. The overall structure of rice Os4BGlu12 is typical of GH1 enzymes, but it contains an extra disulfide bridge in the loop B region. The glucose ring of the G2F in the covalent intermediate was found in a (4)C(1) chair conformation, while that of the noncovalently bound DNP2FG had a (1)S(3) skew boat, consistent with hydrolysis via a (4)H(3) half-chair transition state. The position of the catalytic nucleophile (Glu393) in the G2F structure was more similar to that of the Sinapsis alba myrosinase G2F complex than to that in covalent intermediates of other O-glucosidases, such as rice Os3BGlu6 and Os3BGlu7 beta-glucosidases. This correlated with a significant thioglucosidase activity for Os4BGlu12, although with 200- to 1200-fold lower k(cat)/K(m) values for S-glucosides than the comparable O-glucosides, while hydrolysis of S-glucosides was undetectable for Os3BGlu6 and Os3BGlu7.

The crystal structure of rice (Oryza sativa L.) Os4BGlu12, an oligosaccharide and tuberonic acid glucoside-hydrolyzing beta-glucosidase with significant thioglucohydrolase activity.,Sansenya S, Opassiri R, Kuaprasert B, Chen CJ, Ketudat Cairns JR Arch Biochem Biophys. 2011 Jun 1;510(1):62-72. Epub 2011 Apr 16. PMID:21521631[1]

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

See Also

References

  1. ↑ Sansenya S, Opassiri R, Kuaprasert B, Chen CJ, Ketudat Cairns JR. The crystal structure of rice (Oryza sativa L.) Os4BGlu12, an oligosaccharide and tuberonic acid glucoside-hydrolyzing beta-glucosidase with significant thioglucohydrolase activity. Arch Biochem Biophys. 2011 Jun 1;510(1):62-72. Epub 2011 Apr 16. PMID:21521631 doi:10.1016/j.abb.2011.04.005

3ptm, resolution 2.40Å

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