2VQ5 | pdb_00002vq5

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 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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 Biological Chem 284: 897

  • DOI: https://doi.org/10.1074/jbc.M803738200
  • Primary Citation Related Structures: 
    2VNE, 2VQ5

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 45.91 kDa 
  • Atom Count: 2,806 
  • Modeled Residue Count: 328 
  • Deposited Residue Count: 402 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
S-NORCOCLAURINE SYNTHASE
A, B
201Thalictrum flavumMutation(s): 4 
EC: 4.2.1.78 (PDB Primary Data), 3.5.99.14 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q67A25 (Thalictrum flavum subsp. glaucum)
Explore Q67A25 
Go to UniProtKB:  Q67A25
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ67A25
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LDP

Query on LDP



Download:Ideal Coordinates CCD File
K [auth B]L-DOPAMINE
C8 H11 N O2
VYFYYTLLBUKUHU-UHFFFAOYSA-N
HBA

Query on HBA



Download:Ideal Coordinates CCD File
H [auth A],
L [auth B]
P-HYDROXYBENZALDEHYDE
C7 H6 O2
RGHHSNMVTDWUBI-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D 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 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.474α = 90
b = 86.474β = 90
c = 117.977γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary