8JIJ | pdb_00008jij

Alanine decarboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.222 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.0 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 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.

Macromolecule Content 

  • Total Structure Weight: 48.08 kDa 
  • Atom Count: 3,424 
  • Modeled Residue Count: 411 
  • Deposited Residue Count: 421 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine decarboxylase421Camellia sinensisMutation(s): 0 
Gene Names: TEA_005062
EC: 4.1.1
UniProt
Find proteins for A0A4S4ESS1 (Camellia sinensis var. sinensis)
Explore A0A4S4ESS1 
Go to UniProtKB:  A0A4S4ESS1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4S4ESS1
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.222 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.485α = 90
b = 163.485β = 90
c = 50.203γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release
  • Version 2.0: 2024-12-04
    Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary