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PDBsum entry 1e56

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protein ligands Protein-protein interface(s) links
Glycoside hydrolase PDB id
1e56
Jmol
Contents
Protein chains
490 a.a. *
Ligands
GLC-HBO ×2
Waters ×320
* Residue conservation analysis
PDB id:
1e56
Name: Glycoside hydrolase
Title: Crystal structure of the inactive mutant monocot (maize zmglu1) beta-glucosidase zmglue191d in complex with the natural substrate dimboa-beta-d-glucoside
Structure: Beta-glucosidase. Chain: a, b. Engineered: yes. Mutation: yes
Source: Maize. Strain: cv. Mutin. Tissue: coleoptile. Organelle: chloroplast. Plasmid: pet-21a. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell: plys s cells.
Resolution:
2.10Å     R-factor:   0.228     R-free:   0.267
Authors: M.Czjzek,M.Cicek,D.R.Bevan,V.Zamboni,B.Henrissat,A.Esen
Key ref:
M.Czjzek et al. (2000). The mechanism of substrate (aglycone) specificity in beta -glucosidases is revealed by crystal structures of mutant maize beta -glucosidase-DIMBOA, -DIMBOAGlc, and -dhurrin complexes. Proc Natl Acad Sci U S A, 97, 13555-13560. PubMed id: 11106394 DOI: 10.1073/pnas.97.25.13555
Date:
18-Jul-00     Release date:   11-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P49235  (BGLC_MAIZE) -  4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic
Seq:
Struc:
 
Seq:
Struc:
566 a.a.
490 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 2: E.C.3.2.1.182  - 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. (2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl beta-D-glucopyranoside + H2O = 2,4-dihydroxy-7-methoxy-2H-1,4- benzoxazin-3(4H)-one + D-glucose
2. (2R)-4-hydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl beta-D- glucopyranoside + H2O = 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one + D-glucose
(2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl beta-D-glucopyranoside
+ H(2)O
= 2,4-dihydroxy-7-methoxy-2H-1,4- benzoxazin-3(4H)-one
+ D-glucose
(2R)-4-hydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl beta-D- glucopyranoside
+ H(2)O
= 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one
+ D-glucose
   Enzyme class 3: 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.
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     plastid   2 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.97.25.13555 Proc Natl Acad Sci U S A 97:13555-13560 (2000)
PubMed id: 11106394  
 
 
The mechanism of substrate (aglycone) specificity in beta -glucosidases is revealed by crystal structures of mutant maize beta -glucosidase-DIMBOA, -DIMBOAGlc, and -dhurrin complexes.
M.Czjzek, M.Cicek, V.Zamboni, D.R.Bevan, B.Henrissat, A.Esen.
 
  ABSTRACT  
 
The mechanism and the site of substrate (i.e., aglycone) recognition and specificity were investigated in maize beta-glucosidase (Glu1) by x-ray crystallography by using crystals of a catalytically inactive mutant (Glu1E191D) in complex with the natural substrate 2-O-beta-d-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOAGlc), the free aglycone DIMBOA, and competitive inhibitor para-hydroxy-S-mandelonitrile beta-glucoside (dhurrin). The structures of these complexes and of the free enzyme were solved at 2.1-, 2.1-, 2.0-, and 2.2-A resolution, respectively. The structural data from the complexes allowed us to visualize an intact substrate, free aglycone, or a competitive inhibitor in the slot-like active site of a beta-glucosidase. These data show that the aglycone moiety of the substrate is sandwiched between W378 on one side and F198, F205, and F466 on the other. Thus, specific conformations of these four hydrophobic amino acids and the shape of the aglycone-binding site they form determine aglycone recognition and substrate specificity in Glu1. In addition to these four residues, A467 interacts with the 7-methoxy group of DIMBOA. All residues but W378 are variable among beta-glucosidases that differ in substrate specificity, supporting the conclusion that these sites are the basis of aglycone recognition and binding (i.e., substrate specificity) in beta-glucosidases. The data also provide a plausible explanation for the competitive binding of dhurrin to maize beta-glucosidases with high affinity without being hydrolyzed.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Structure of the ligands and the active site of Glu1E191D. (A) The natural substrate DIMBOAGlc (Left), the aglycone DIMBOA (Center), and the competitive inhibitor dhurrin (Right). (B) Ribbon diagram of the structure of the maize -glucosidase Glu1 and its inactive Glu1E191D mutant, showing the catalytic residues E191 (D191 in the mutant) and E406 (red), four residues (F198, F205, W378, and F466) forming the aglycone-binding pocket (blue), and two other residues (A467 and Y473) that are probably important for aglycone recognition (yellow). Different colors and the color transitions in -helices and -strands trace the polypeptide backbone in the barrel-shaped three-dimensional structure from the N terminus (dark blue) to the C terminus (dark red) direction. The figure was produced with MOLSCRIPT (35) and RASTER3D (36). (C) Electrostatic surface representation of the active site region of Glu1E191D showing positively charged regions in blue, negatively charged regions in red, and neutral regions in white. The slot-like active site, measuring 23 Å × 7.1 Å at the entrance, contains the natural substrate DIMBOAGlc in compact representation with standard atom-type colors. In this view, only the aglycone moiety is visible in its binding site as glucose is hidden below aglycone. C was produced with GRASP (37).
Figure 3.
Fig. 3. Aglycone recognition and binding in -glycosidases as revealed by DIMBOAGlc-, DIMBOA-, and dhurrin-Glu1E191D inactive mutant complexes. (A) Closeup view of the active site of Glu1, showing the catalytic glutamates E191 and E406 (red), the four residues (F198, F205, W378, and F466) forming the aglycone-binding pocket (light blue), and the additional residues (A467 and Y473) that are probably important for aglycone recognition (light green). (B) Glu1E191D with bound DIMBOAGlc. The glycone moiety is in blue, whereas the aglycone is in atom-type colors. The bulky aryl group is sandwiched between W378 on one side and F198, F205, and F466 on the other. (C) Same as B but with bound DIMBOA, showing a slightly different orientation than DIMBOA in DIMBOAGlc, which is constrained by the glycosidic linkage. (D) Same as B but with bound dhurrin. The aglycone moiety of the inhibitor dhurrin is in the same position as the aglycone of the natural substrate. Figs. 3. and 4 were produced with TURBO-FRODO (38).
 
  Figures were selected by an automated process.  

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.  
20925655 V.Lombard, T.Bernard, C.Rancurel, H.Brumer, P.M.Coutinho, and B.Henrissat (2010).
A hierarchical classification of polysaccharide lyases for glycogenomics.
  Biochem J, 432, 437-444.  
18074341 A.D.Hill, and P.J.Reilly (2008).
A Gibbs free energy correlation for automated docking of carbohydrates.
  J Comput Chem, 29, 1131-1141.  
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.  
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.  
17196101 R.Opassiri, B.Pomthong, T.Onkoksoong, T.Akiyama, A.Esen, and J.R.Ketudat Cairns (2006).
Analysis of rice glycosyl hydrolase family 1 and expression of Os4bglu12 beta-glucosidase.
  BMC Plant Biol, 6, 33.  
  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.  
15062085 J.Allouch, W.Helbert, B.Henrissat, and M.Czjzek (2004).
Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.
  Structure, 12, 623-632.
PDB code: 1urx
15604686 Z.Xu, L.Escamilla-Treviño, L.Zeng, M.Lalgondar, D.Bevan, B.Winkel, A.Mohamed, C.L.Cheng, M.C.Shih, J.Poulton, and A.Esen (2004).
Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 1.
  Plant Mol Biol, 55, 343-367.  
12964193 A.Laederach, and P.J.Reilly (2003).
Specific empirical free energy function for automated docking of carbohydrates to proteins.
  J Comput Chem, 24, 1748-1757.  
12012341 B.Cobucci-Ponzano, M.Moracci, B.Di Lauro, M.Ciaramella, R.D'Avino, and M.Rossi (2002).
Ionic network at the C-terminus of the beta-glycosidase from the hyperthermophilic archaeon Sulfolobus solfataricus: Functional role in the quaternary structure thermal stabilization.
  Proteins, 48, 98.  
12487426 Y.Bhatia, S.Mishra, and V.S.Bisaria (2002).
Microbial beta-glucosidases: cloning, properties, and applications.
  Crit Rev Biotechnol, 22, 375-407.  
11785761 Y.Bourne, and B.Henrissat (2001).
Glycoside hydrolases and glycosyltransferases: families and functional modules.
  Curr Opin Struct Biol, 11, 593-600.  
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. Where a reference describes a PDB structure, the PDB code is shown on the right.