3AC0

Crystal structure of Beta-glucosidase from Kluyveromyces marxianus in complex with glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Role of a PA14 domain in determining substrate specificity of a glycoside hydrolase family 3 beta-glucosidase from Kluyveromyces marxianus.

Yoshida, E.Hidaka, M.Fushinobu, S.Koyanagi, T.Minami, H.Tamaki, H.Kitaoka, M.Katayama, T.Kumagai, H.

(2010) Biochem.J. 431: 39-49

  • DOI: 10.1042/BJ20100351
  • Primary Citation of Related Structures:  3ABZ

  • PubMed Abstract: 
  • β-Glucosidase from Kluyveromyces marxianus (KmBglI) belongs to the GH3 (glycoside hydrolase family 3). The enzyme is particularly unusual in that a PA14 domain (pf07691), for which a carbohydrate-binding role has been claimed, is inserted into the ca ...

    β-Glucosidase from Kluyveromyces marxianus (KmBglI) belongs to the GH3 (glycoside hydrolase family 3). The enzyme is particularly unusual in that a PA14 domain (pf07691), for which a carbohydrate-binding role has been claimed, is inserted into the catalytic core sequence. In the present study, we determined the enzymatic properties and crystal structure of KmBglI in complex with glucose at a 2.55 A (1 A=0.1 nm) resolution. A striking characteristic of KmBglI was that the enzyme activity is essentially limited to disaccharides, and when trisaccharides were used as the substrates the activity was drastically decreased. This chain-length specificity is in sharp contrast with the preferred action on oligosaccharides of barley β-D-glucan glucohydrolase (ExoI), which does not have a PA14 domain insertion. The structure of subsite (-1) of KmBglI is almost identical with that of Thermotoga neapolitana β-glucosidase and is also similar to that of ExoI, however, the structures of subsite (+1) significantly differ among them. In KmBglI, the loops extending from the PA14 domain cover the catalytic pocket to form subsite (+1), and hence simultaneously become a steric hindrance that could limit the chain length of the substrates to be accommodated. Mutational studies demonstrated the critical role of the loop regions in determining the substrate specificity. The active-site formation mediated by the PA14 domain of KmBglI invokes α-complementation of β-galactosidase exerted by its N-terminal domain, to which the PA14 domain shows structural resemblance. The present study is the first which reveals the structural basis of the interaction between the PA14 domain and a carbohydrate.


    Related Citations: 
    • Purification, crystallization and preliminary X-ray analysis of beta-glucosidase from Kluyveromyces marxianus NBRC1777
      Yoshida, E.,Hidaka, M.,Fushinobu, S.,Koyanagi, T.,Minami, H.,Tamaki, H.,Kitaoka, M.,Katayama, T.,Kumagai, H.
      (2009) Acta Crystallogr.,Sect.F 65: 1190


    Organizational Affiliation

    Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-glucosidase I
A, B, C, D
845Kluyveromyces marxianusGene Names: Bgl
EC: 3.2.1.21
Find proteins for D1GCC6 (Kluyveromyces marxianus)
Go to UniProtKB:  D1GCC6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A, B, C, D
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 245.847α = 90.00
b = 148.412β = 112.84
c = 119.642γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
SOLVEphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-10-30
    Type: Database references