PDBsum entry: 1v02

Hydrolase

PDB-id: 1v02

Asymmetric unit

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Description

Header details

Header records

References

PROCHECK

Protein chains

484 a.a. *

Waters ×5068

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit, dimer
- as defined in PDB file (see also PQS)

PDB id:

1v02

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

Biological unit:

Dimer (from PDB file)

UniProt:

Chains A, B, C, D, E, F: Q41290 (Q41290_SORBI)

Seq:

Struc:

Seq:

Struc:

Seq:

565 a.a.

Struc:

484 a.a.*

Key:	PfamA domain	PfamB domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Resolution:

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]

Date:

22-Mar-04

Release date:

20-May-04

Related entries:

1v03
crystal structure of the sorghum bicolor dhurrinase 1

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Key reference

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.

ABSTRACT

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.