8JG7 | pdb_00008jg7

Serine decarboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.262 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure and evolution of alanine/serine decarboxylases and the engineering of theanine production.

Wang, H.Zhu, B.Qiao, S.Dong, C.Wan, X.Gong, W.Zhang, Z.

(2024) Elife 12

  • DOI: https://doi.org/10.7554/eLife.91046
  • Primary Citation of Related Structures:  
    8JG7, 8JIJ, 8JIK

  • PubMed Abstract: 

    Ethylamine (EA), the precursor of theanine biosynthesis, is synthesized from alanine decarboxylation by alanine decarboxylase (AlaDC) in tea plants. AlaDC evolves from serine decarboxylase (SerDC) through neofunctionalization and has lower catalytic activity. However, lacking structure information hinders the understanding of the evolution of substrate specificity and catalytic activity. In this study, we solved the X-ray crystal structures of AlaDC from Camellia sinensis (CsAlaDC) and SerDC from Arabidopsis thaliana (AtSerDC). Tyr 341 of AtSerDC or the corresponding Tyr 336 of CsAlaDC is essential for their enzymatic activity. Tyr 111 of AtSerDC and the corresponding Phe 106 of CsAlaDC determine their substrate specificity. Both CsAlaDC and AtSerDC have a distinctive zinc finger and have not been identified in any other Group II PLP-dependent amino acid decarboxylases. Based on the structural comparisons, we conducted a mutation screen of CsAlaDC. The results indicated that the mutation of L110F or P114A in the CsAlaDC dimerization interface significantly improved the catalytic activity by 110% and 59%, respectively. Combining a double mutant of CsAlaDC L110F/P114A with theanine synthetase increased theanine production 672% in an in vitro system. This study provides the structural basis for the substrate selectivity and catalytic activity of CsAlaDC and AtSerDC and provides a route to more efficient biosynthesis of theanine.


  • Organizational Affiliation
    • Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine decarboxylaseA,
B [auth C],
C [auth D],
D [auth E]
418Arabidopsis thalianaMutation(s): 0 
Gene Names: SDCEMB1075SDC1At1g43710F2J6.7
EC: 4.1.1
UniProt
Find proteins for Q9MA74 (Arabidopsis thaliana)
Explore Q9MA74 
Go to UniProtKB:  Q9MA74
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9MA74
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth C],
K [auth D],
N [auth E]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
J [auth C],
M [auth D],
P [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
I [auth C],
L [auth D],
O [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.36α = 90
b = 149.45β = 109.18
c = 139.126γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-12-04
    Changes: Database references, Structure summary