2WFL | pdb_00002wfl

Crystal structure of polyneuridine aldehyde esterase

• PDB DOI: https://doi.org/10.2210/pdb2WFL/pdb

• Classification: HYDROLASE
• Organism(s): Rauvolfia serpentina
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.231 (Depositor), 0.423 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.385 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

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

• PubMed: 19496101 
• DOI: https://doi.org/10.1002/anie.200900150
• Primary Citation 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 generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 59.8 kDa 
• Atom Count: 4,347 
• Modeled Residue Count: 510 
• Deposited Residue Count: 528 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POLYNEURIDINE-ALDEHYDE ESTERASE	A	264	Rauvolfia serpentina	Mutation(s): 0  EC: 3.1.1.78
UniProt
Find proteins for Q9SE93 (Rauvolfia serpentina) Explore Q9SE93  Go to UniProtKB:  Q9SE93

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
POLYNEURIDINE-ALDEHYDE ESTERASE	B	264	Rauvolfia serpentina	Mutation(s): 0  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
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.231 (Depositor), 0.423 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.385 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.758	α = 90
b = 176.917	β = 90
c = 75.697	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
Auto-Rickshaw	phasing
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Derived calculations
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary