Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 109.95 kDa 
• Atom Count: 7655 
• Modelled Residue Count: 937 
• Deposited Residue Count: 980 
• Unique protein chains: 1

6EEI

Crystal structure of Arabidopsis thaliana phenylacetaldehyde synthase in complex with L-phenylalanine

• PDB DOI: 10.2210/pdb6EEI/pdb

• Classification: LYASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-14 Released: 2018-09-19 
• Deposition Author(s): Torrens-Spence, M.P., Chiang, Y., Smith, T., Vicent, M.A., Wang, Y., Weng, J.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.240 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 

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

• PubMed: 32371491 
• DOI: 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.

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Related Citations: 

• Structural basis for independent origins of new catalytic machineries in plant AAAD proteins
  Torrens-Spence, M.P., Chiang, Y.-C., Smith, T., Vicent, M.A., Wang, Y., Weng, J.K.
  (2019) Biorxiv --: --

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Organizational Affiliation: 

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine decarboxylase 1	A, B	490	Arabidopsis thaliana	Mutation(s): 0  Gene Names: ELI5, At2g20340, F11A3.11, AADC, AAS EC: 4.1.1.25 (PDB Primary Data), 4.1.1.109 (UniProt), 4.1.1.107 (UniProt)
UniProt
Find proteins for Q8RY79 (Arabidopsis thaliana) Explore Q8RY79  Go to UniProtKB:  Q8RY79

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PHE	D [auth A], F [auth B]	PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-QMMMGPOBSA-N
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.240 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.064	α = 90
b = 106.791	β = 90
c = 115.903	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-08-14 
• Released Date: 2018-09-19 
Deposition Author(s): Torrens-Spence, M.P., Chiang, Y., Smith, T., Vicent, M.A., Wang, Y., Weng, J.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41 GM103403

Revision History  

• 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