Structures of Alkaloid Biosynthetic Glucosidases Decode Substrate Specificity

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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Structures of alkaloid biosynthetic glucosidases decode substrate specificity.

Xia, L.Ruppert, M.Wang, M.Panjikar, S.Lin, H.Rajendran, C.Barleben, L.Stockigt, J.

(2012) ACS Chem Biol 7: 226-234

  • DOI: https://doi.org/10.1021/cb200267w
  • Primary Citation of Related Structures:  
    3U57, 3U5U, 3U5Y, 4A3Y

  • PubMed Abstract: 

    Two similar enzymes with different biosynthetic function in one species have evolved to catalyze two distinct reactions. X-ray structures of both enzymes help reveal their most important differences. The Rauvolfia alkaloid biosynthetic network harbors two O-glucosidases: raucaffricine glucosidase (RG), which hydrolyses raucaffricine to an intermediate downstream in the ajmaline pathway, and strictosidine glucosidase (SG), which operates upstream. RG converts strictosidine, the substrate of SG, but SG does not accept raucaffricine. Now elucidation of crystal structures of RG, inactive RG-E186Q mutant, and its complexes with ligands dihydro-raucaffricine and secologanin reveals that it is the "wider gate" of RG that allows strictosidine to enter the catalytic site, whereas the "slot-like" entrance of SG prohibits access by raucaffricine. Trp392 in RG and Trp388 in SG control the gate shape and acceptance of substrates. Ser390 directs the conformation of Trp392. 3D structures, supported by site-directed mutations and kinetic data of RG and SG, provide a structural and catalytic explanation of substrate specificity and deeper insights into O-glucosidase chemistry.

  • Organizational Affiliation

    Institute of Materia Medica, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, PR China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
513Rauvolfia serpentinaMutation(s): 1 
Gene Names: RGVGT
EC: (PDB Primary Data), (UniProt)
Find proteins for Q9SPP9 (Rauvolfia serpentina)
Explore Q9SPP9 
Go to UniProtKB:  Q9SPP9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SPP9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.927α = 90
b = 129.203β = 90
c = 216.798γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Database references, Derived calculations, Structure summary