3GZJ

Crystal Structure of Polyneuridine Aldehyde Esterase Complexed with 16-epi-Vellosimine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural basis and enzymatic mechanism of the biosynthesis of C9- from C10-monoterpenoid indole alkaloids

Yang, L.Hill, M.Wang, M.Panjikar, S.Stockigt, J.

(2009) Angew Chem Int Ed Engl 48: 5211-5213

  • DOI: https://doi.org/10.1002/anie.200900150
  • Primary Citation of Related Structures:  
    2WFL, 2WFM, 3GZJ

  • PubMed Abstract: 

    Cutting carbons: The three-dimensional structure of polyneuridine aldehyde esterase (PNAE) gives insight into the enzymatic mechanism of the biosynthesis of C(9)- from C(10)-monoterpenoid indole alkaloids (see scheme). PNAE is a very substrate-specific serine esterase. It harbors the catalytic triad S87-D216-H244, and is a new member of the alpha/beta-fold hydrolase superfamily. Its novel function leads to the diversification of alkaloid structures.


  • Organizational Affiliation

    Institute of Materia Medica, College of Pharmaceutical Sciences, Zhejiang University, 383 Yu Hang Tang Road, Hangzhou 310058, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyneuridine-aldehyde esterase
A, B, C, D, E
258Rauvolfia serpentinaMutation(s): 1 
EC: 3.1.1.78
UniProt
Find proteins for Q9SE93 (Rauvolfia serpentina)
Explore Q9SE93 
Go to UniProtKB:  Q9SE93
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SE93
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.21α = 90
b = 44.61β = 104.44
c = 180.41γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description