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PDBsum entry 1e1f

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1e1f
Jmol
Contents
Protein chains
490 a.a. *
Ligands
PSG ×2
Waters ×356
* Residue conservation analysis
PDB id:
1e1f
Name: Hydrolase
Title: Crystal structure of a monocot (maize zmglu1) beta-glucosidase in complex with p-nitrophenyl-beta-d-thioglucoside
Structure: Beta-glucosidase. Chain: a, b. Engineered: yes
Source: Zea mays. Maize. Organism_taxid: 4577. Strain: cv. Mutin. Tissue: coleoptile. Organelle: chloroplast. Plasmid: pet-21a. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.60Å     R-factor:   0.199     R-free:   0.252
Authors: M.Czjzek,M.Cicek,D.R.Bevan,B.Henrissat,A.Esen
Key ref: M.Czjzek et al. (2001). Crystal structure of a monocotyledon (maize ZMGlu1) beta-glucosidase and a model of its complex with p-nitrophenyl beta-D-thioglucoside. Biochem J, 354, 37-46. PubMed id: 11171077
Date:
03-May-00     Release date:   19-Feb-01    
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

 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    
 
 
Biochem J 354:37-46 (2001)
PubMed id: 11171077  
 
 
Crystal structure of a monocotyledon (maize ZMGlu1) beta-glucosidase and a model of its complex with p-nitrophenyl beta-D-thioglucoside.
M.Czjzek, M.Cicek, V.Zamboni, W.P.Burmeister, D.R.Bevan, B.Henrissat, A.Esen.
 
  ABSTRACT  
 
The maize beta-glucosidase isoenzymes ZMGlu1 and ZMGlu2 hydrolyse the abundant natural substrate DIMBOAGlc (2-O-beta-D-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxazin-3-one), whose aglycone DIMBOA (2,4-hydroxy-7-methoxy-1,4-benzoxazin-3-one) is the major defence chemical protecting seedlings and young plant parts against herbivores and other pests. The two isoenzymes hydrolyse DIMBOAGlc with similar kinetics but differ from each other and their sorghum homologues with respect to specificity towards other substrates. To gain insights into the mechanism of substrate (i.e. aglycone) specificity between the two maize isoenzymes and their sorghum homologues, ZMGlu1 was produced in Escherichia coli, purified, crystallized and its structure solved at 2.5 Angstrom resolution by X-ray crystallography. In addition, the complex of ZMGlu1 with the non-hydrolysable inhibitor p-nitrophenyl beta-D-thioglucoside was crystallized and, based on the partial electron density, a model for the inhibitor molecule within the active site is proposed. The inhibitor is located in a slot-like active site where its aromatic aglycone is held by stacking interactions with Trp-378. Whereas some of the atoms on the non-reducing end of the glucose moiety can be modelled on the basis of the electron density, most of the inhibitor atoms are highly disordered. This is attributed to the requirement of the enzyme to accommodate two different species, namely the substrate in its ground state and in its distorted conformation, for catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20544971 C.Nagao, N.Nagano, and K.Mizuguchi (2010).
Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies.
  Proteins, 78, 2369-2384.  
20490603 J.R.Ketudat Cairns, and A.Esen (2010).
β-Glucosidases.
  Cell Mol Life Sci, 67, 3389-3405.  
18953653 A.Kumar, N.K.Singhal, B.Ramanujam, A.Mitra, N.R.Rameshwaram, S.K.Nadimpalli, and C.P.Rao (2009).
C(1)-/C(2)-aromatic-imino-glyco-conjugates: experimental and computational studies of binding, inhibition and docking aspects towards glycosidases isolated from soybean and jack bean.
  Glycoconj J, 26, 495-510.  
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.  
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.
PDB code: 1uwi
17009294 K.Krause, and E.Kothe (2006).
Use of RNA fingerprinting to identify fungal genes specifically expressed during ectomycorrhizal interaction.
  J Basic Microbiol, 46, 387-399.  
15930622 X.Ma, J.Koepke, A.Bayer, G.Fritzsch, H.Michel, and J.Stöckigt (2005).
Crystallization and preliminary X-ray analysis of native and selenomethionyl vinorine synthase from Rauvolfia serpentina.
  Acta Crystallogr D Biol Crystallogr, 61, 694-696.  
14660638 J.K.McCarthy, A.Uzelac, D.F.Davis, and D.E.Eveleigh (2004).
Improved catalytic efficiency and active site modification of 1,4-beta-D-glucan glucohydrolase A from Thermotoga neapolitana by directed evolution.
  J Biol Chem, 279, 11495-11502.  
15148317 L.Verdoucq, J.Morinière, D.R.Bevan, A.Esen, A.Vasella, B.Henrissat, and M.Czjze (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.
PDB codes: 1v02 1v03 1v08
12596260 E.Bismuto, F.Febbraio, S.Limongelli, R.Briante, and R.Nucci (2003).
Dynamic fluorescence studies of beta-glycosidase mutants from Sulfolobus solfataricus: effects of single mutations on protein thermostability.
  Proteins, 51, 10-20.  
12684498 L.Verdoucq, M.Czjzek, J.Moriniere, D.R.Bevan, and A.Esen (2003).
Mutational and structural analysis of aglycone specificity in maize and sorghum beta-glucosidases.
  J Biol Chem, 278, 25055-25062.
PDB code: 1h49
12837801 X.Wang, X.He, S.Yang, X.An, W.Chang, and D.Liang (2003).
Structural basis for thermostability of beta-glycosidase from the thermophilic eubacterium Thermus nonproteolyticus HG102.
  J Bacteriol, 185, 4248-4255.
PDB code: 1np2
11900558 T.Kaper, H.H.van Heusden, B.van Loo, A.Vasella, J.van der Oost, and W.M.de Vos (2002).
Substrate specificity engineering of beta-mannosidase and beta-glucosidase from Pyrococcus by exchange of unique active site residues.
  Biochemistry, 41, 4147-4155.  
12487426 Y.Bhatia, S.Mishra, and V.S.Bisaria (2002).
Microbial beta-glucosidases: cloning, properties, and applications.
  Crit Rev Biotechnol, 22, 375-407.  
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.