3GZJ

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

• PDB DOI: https://doi.org/10.2210/pdb3GZJ/pdb

• Classification: HYDROLASE
• Organism(s): Rauvolfia serpentina
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-04-07 Released: 2009-08-18 
• Deposition Author(s): Yang, L., Hill, M., Wang, M., Panjikar, S., Stoeckigt, J.

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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

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

• PubMed: 19496101 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Macromolecule Content

• Total Structure Weight: 146.23 kDa 
• Atom Count: 10,318 
• Modelled Residue Count: 1,270 
• Deposited Residue Count: 1,290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyneuridine-aldehyde esterase	A, B, C, D, E	258	Rauvolfia serpentina	Mutation(s): 1  EC: 3.1.1.78
UniProt
Find proteins for Q9SE93 (Rauvolfia serpentina) Explore Q9SE93  Go to UniProtKB:  Q9SE93

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EVS	F [auth A], G [auth B], H [auth C], I [auth D]	16-epi-Vellosimine C19 H20 N2 O MHASSCPGKAMILD-MIOJWWSHSA-N

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 = 171.21	α = 90
b = 44.61	β = 104.44
c = 180.41	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Yang, L., Hill, M., Wang, M., Panjikar, S., Stoeckigt, J.

Revision History  

• 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