6EEM

Crystal structure of Papaver somniferum tyrosine decarboxylase in complex with L-tyrosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

Starting Model: experimental
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This is version 1.6 of the entry. See complete history


Literature

Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins.

Torrens-Spence, M.P.Chiang, Y.C.Smith, T.Vicent, M.A.Wang, Y.Weng, J.K.

(2020) Proc Natl Acad Sci U S A 117: 10806-10817

  • DOI: https://doi.org/10.1073/pnas.1920097117
  • Primary Citation of Related Structures:  
    6EEI, 6EEM, 6EEQ, 6EEW

  • PubMed Abstract: 

    Radiation of the plant pyridoxal 5'-phosphate (PLP)-dependent aromatic l-amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic l-amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. Here, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.


  • Organizational Affiliation

    Whitehead Institute for Biomedical Research, Cambridge, MA 02142.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine/dopa decarboxylase512Papaver somniferumMutation(s): 0 
Gene Names: tydc9
EC: 4.1.1.28
UniProt
Find proteins for O82415 (Papaver somniferum)
Explore O82415 
Go to UniProtKB:  O82415
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO82415
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine/dopa decarboxylase512Papaver somniferumMutation(s): 0 
Gene Names: tydc9
EC: 4.1.1.28
UniProt
Find proteins for O82415 (Papaver somniferum)
Explore O82415 
Go to UniProtKB:  O82415
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO82415
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0PR
Query on 0PR

Download Ideal Coordinates CCD File 
C [auth A]N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-tyrosine
C17 H21 N2 O8 P
AGEIFYRIXWJCET-HNNXBMFYSA-N
TYR
Query on TYR

Download Ideal Coordinates CCD File 
H [auth B]TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.771α = 90
b = 122.771β = 90
c = 166.998γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103403

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2020-05-20
    Changes: Database references
  • Version 1.4: 2020-06-03
    Changes: Database references
  • Version 1.5: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.6: 2023-11-15
    Changes: Data collection