2VQ5

X-ray structure of Norcoclaurine synthase from Thalictrum flavum in complex with dopamine and hydroxybenzaldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of Enzymatic S-Norcoclaurine Biosynthesis.

Ilari, A.Franceschini, S.Bonamore, A.Arenghi, F.Botta, B.Macone, A.Pasquo, A.Bellucci, L.Boffi, A.

(2009) J.Biol.Chem. 284: 897

  • DOI: 10.1074/jbc.M803738200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The enzyme norcoclaurine synthase (NCS) catalyzes the stereospecific Pictet-Spengler cyclization between dopamine and 4-hydroxyphenylacetaldehyde, the key step in the benzylisoquinoline alkaloid biosynthetic pathway. The crystallographic structure of ...

    The enzyme norcoclaurine synthase (NCS) catalyzes the stereospecific Pictet-Spengler cyclization between dopamine and 4-hydroxyphenylacetaldehyde, the key step in the benzylisoquinoline alkaloid biosynthetic pathway. The crystallographic structure of norcoclaurine synthase from Thalictrum flavum in its complex with dopamine substrate and the nonreactive substrate analogue 4-hydroxybenzaldehyde has been solved at 2.1A resolution. NCS shares no common features with the functionally correlated "Pictet-Spenglerases" that catalyze the first step of the indole alkaloids pathways and conforms to the overall fold of the Bet v1-like protein. The active site of NCS is located within a 20-A-long catalytic tunnel and is shaped by the side chains of a tyrosine, a lysine, an aspartic, and a glutamic acid. The geometry of the amino acid side chains with respect to the substrates reveals the structural determinants that govern the mechanism of the stereoselective Pictet-Spengler cyclization, thus establishing an excellent foundation for the understanding of the finer details of the catalytic process. Site-directed mutations of the relevant residues confirm the assignment based on crystallographic findings.


    Organizational Affiliation

    Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari, CNR, Sapienza University, Piazzale Aldo Moro 5, 00185 Roma, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
S-NORCOCLAURINE SYNTHASE
A, B
201Thalictrum flavum subsp. glaucumMutation(s): 4 
EC: 4.2.1.78
Find proteins for Q67A25 (Thalictrum flavum subsp. glaucum)
Go to UniProtKB:  Q67A25
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LDP
Query on LDP

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Download CCD File 
B
L-DOPAMINE
DOPAMINE
C8 H11 N O2
VYFYYTLLBUKUHU-UHFFFAOYSA-N
 Ligand Interaction
HBA
Query on HBA

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Download CCD File 
A, B
P-HYDROXYBENZALDEHYDE
C7 H6 O2
RGHHSNMVTDWUBI-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 86.474α = 90.00
b = 86.474β = 90.00
c = 117.977γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance