PDBsum entry 1v02

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Hydrolase PDB id
Protein chains
(+ 0 more) 484 a.a. *
Waters ×5068
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of the sorghum bicolor dhurrinase 1
Structure: Dhurrinase. Chain: a, b, c, d, f. Synonym: dhurrinase-1. Engineered: yes. Dhurrinase. Chain: e. Synonym: dhurrinase-1. Engineered: yes
Source: Sorghum bicolor. Sorghum. Organism_taxid: 4558. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
1.9Å     R-factor:   0.173     R-free:   0.210
Authors: J.Moriniere,L.Verdoucq,D.R.Bevan,A.Esen,B.Henrissat, M.Czjzek
Key ref:
L.Verdoucq et al. (2004). Structural determinants of substrate specificity in family 1 beta-glucosidases: novel insights from the crystal structure of sorghum dhurrinase-1, a plant beta-glucosidase with strict specificity, in complex with its natural substrate. J Biol Chem, 279, 31796-31803. PubMed id: 15148317 DOI: 10.1074/jbc.M402918200
22-Mar-04     Release date:   20-May-04    
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Protein chains
Pfam   ArchSchema ?
Q41290  (Q41290_SORBI) -  Dhurrinase
565 a.a.
484 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     3 terms  


DOI no: 10.1074/jbc.M402918200 J Biol Chem 279:31796-31803 (2004)
PubMed id: 15148317  
Structural determinants of substrate specificity in family 1 beta-glucosidases: novel insights from the crystal structure of sorghum dhurrinase-1, a plant beta-glucosidase with strict specificity, in complex with its natural substrate.
L.Verdoucq, J.Morinière, D.R.Bevan, A.Esen, A.Vasella, B.Henrissat, M.Czjze.
Plant beta-glucosidases play a crucial role in defense against pests. They cleave, with variable specificity, beta-glucosides to release toxic aglycone moieties. The Sorghum bicolor beta-glucosidase isoenzyme Dhr1 has a strict specificity for its natural substrate dhurrin (p-hydroxy-(S)-mandelonitrile-beta-D-glucoside), whereas its close homolog, the maize beta-glucosidase isoenzyme Glu1, which shares 72% sequence identity, hydrolyzes a broad spectrum of substrates in addition to its natural substrate 2-O-beta-D-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxaxin-3-one. Structural data from enzyme.substrate complexes of Dhr1 show that the mode of aglycone binding differs from that previously observed in the homologous maize enzyme. Specifically, the data suggest that Asn(259), Phe(261), and Ser(462), located in the aglycone-binding site of S. bicolor Dhr1, are crucial for aglycone recognition and binding. The tight binding of the aglycone moiety of dhurrin promotes the stabilization of the reaction intermediate in which the glycone moiety is in a deformed (1)S(3) conformation within the glycone-binding site, ready for nucleophilic attack to occur. Compared with the broad specificity maize beta-glucosidase, this different binding mode explains the narrow specificity of sorghum dhurrinase-1.
  Selected figure(s)  
Figure 4.
FIG. 4. Dhurrin bound in the active sites to SbDhr1-E189D and glucotetrazole bound to ZmGlu1-E191D. A, electron density surrounding the dhurrin molecule in the active site of SbDhr1-E189D. The 2F[o] - F[c] Fourier difference maps at the final stage of refinement are shown contoured at 1 above the mean density. B, a slice in the surface representation of SbDhr1 in complex with dhurrin showing the cyano group-binding pocket. The dipole moment of the polar pocket, calculated with GRASP (28), coincides with that of the cyano group. C, electron density around the glucotetrazole molecule in the active site of ZmGlu1-E191D. The F[o] - F[c] Fourier difference maps before refinement are shown, calculated using only the enzyme model phases without substrate, contoured at 2.5 above the mean density. D, superimposition of the active sites of myrosinase (blue) and ZmGlu1 (yellow), both in complex with the glucotetrazole inhibitor molecule.
Figure 5.
FIG. 5. Superimposition of the glucose moieties of DIMBOA-Glc in ZmGlu1 and dhurrin in SbDhr1. The glucose ring of DIM-BOA-Glc has rotated by 60° with respect to that of dhurrin. Consequently, the residues binding the sugar groups O-2, O-3, and O-4 in dhurrin bind O-3, O-4, and O-6 in DIMBOA-Glc. See also Table III. In each box, the top residue occurs in ZmGlu1, and the bottom residue occurs in SbDhr1. Of the 2 glutamates shown by stick representation, Glu464 occurs in ZmGlu1, whereas Glu460 occurs in SbDhr1.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 31796-31803) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20490603 J.R.Ketudat Cairns, and A.Esen (2010).
  Cell Mol Life Sci, 67, 3389-3405.  
18615662 A.D.Hill, and P.J.Reilly (2008).
Computational analysis of glycoside hydrolase family 1 specificities.
  Biopolymers, 89, 1021-1031.  
18422657 L.M.Mendonça, and S.R.Marana (2008).
The role in the substrate specificity and catalysis of residues forming the substrate aglycone-binding site of a beta-glycosidase.
  FEBS J, 275, 2536-2547.  
19016858 R.Dopitová, P.Mazura, L.Janda, R.Chaloupková, P.Jerábek, J.Damborský, T.Filipi, N.S.Kiran, and B.Brzobohatý (2008).
Functional analysis of the aglycone-binding site of the maize beta-glucosidase Zm-p60.1.
  FEBS J, 275, 6123-6135.  
18046575 Z.Minic (2008).
Physiological roles of plant glycoside hydrolases.
  Planta, 227, 723-740.  
18033585 J.Stöckigt, and S.Panjikar (2007).
Structural biology in plant natural product biosynthesis--architecture of enzymes from monoterpenoid indole and tropane alkaloid biosynthesis.
  Nat Prod Rep, 24, 1382-1400.  
17503162 M.León, P.Isorna, M.Menéndez, J.Sanz-Aparicio, and J.Polaina (2007).
Comparative study and mutational analysis of distinctive structural elements of hyperthermophilic enzymes.
  Protein J, 26, 435-444.  
16609814 B.Di Lauro, M.Rossi, and M.Moracci (2006).
Characterization of a beta-glycosidase from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius.
  Extremophiles, 10, 301-310.  
  16880561 W.Chuenchor, S.Pengthaisong, J.Yuvaniyama, R.Opassiri, J.Svasti, and J.R.Ketudat Cairns (2006).
Purification, crystallization and preliminary X-ray analysis of rice BGlu1 beta-glucosidase with and without 2-deoxy-2-fluoro-beta-D-glucoside.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 798-801.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.