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PDBsum entry 3gnp

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protein ligands links
Hydrolase PDB id
3gnp
Jmol
Contents
Protein chain
478 a.a. *
Ligands
SOG
GOL ×4
Waters ×340
* Residue conservation analysis
PDB id:
3gnp
Name: Hydrolase
Title: Crystal structure of a rice os3bglu6 beta-glucosidase with o d-thio-glucoside
Structure: Os03g0212800 protein. Chain: a. Fragment: unp residues 38-521. Synonym: beta-glucosidase, glycosyl hydrolase family 1 prot expressed. Engineered: yes
Source: Oryza sativa subsp. Japonica. Rice. Organism_taxid: 39947. Gene: loc_os03g11420, os03g0212800, os3bglu6 locus id: os03 expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.180     R-free:   0.207
Authors: S.Seshadri,T.Akiyama,R.Opassiri,B.Kuaprasert,J.R.K.Cairns
Key ref: S.Seshadri et al. (2009). Structural and enzymatic characterization of Os3BGlu6, a rice beta-glucosidase hydrolyzing hydrophobic glycosides and (1->3)- and (1->2)-linked disaccharides. Plant Physiol, 151, 47-58. PubMed id: 19587102 DOI: 10.1104/pp.109.139436
Date:
17-Mar-09     Release date:   21-Jul-09    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8L7J2  (BGL06_ORYSJ) -  Beta-glucosidase 6
Seq:
Struc:
 
Seq:
Struc:
521 a.a.
478 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.21  - Beta-glucosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     10 terms  

 

 
DOI no: 10.1104/pp.109.139436 Plant Physiol 151:47-58 (2009)
PubMed id: 19587102  
 
 
Structural and enzymatic characterization of Os3BGlu6, a rice beta-glucosidase hydrolyzing hydrophobic glycosides and (1->3)- and (1->2)-linked disaccharides.
S.Seshadri, T.Akiyama, R.Opassiri, B.Kuaprasert, J.K.Cairns.
 
  ABSTRACT  
 
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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20490603 J.R.Ketudat Cairns, and A.Esen (2010).
β-Glucosidases.
  Cell Mol Life Sci, 67, 3389-3405.  
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