9RJ1 | pdb_00009rj1

S-methylcysteine synthase (BSAS4) from common bean in complex with PLP, BEZ, and GOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.168 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.141 (Depositor), 0.143 (DCC) 
  • R-Value Observed: 
    0.142 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Benzoic and salicylic acids inhibit beta-substituted alanine synthase 4;1 in common bean.

Lu, Z.Witek, W.Ruszkowski, M.Imiolczyk, B.Paulish, N.Joshi, J.Jaskolski, M.Marsolais, F.

(2025) Plant Physiol 199

  • DOI: https://doi.org/10.1093/plphys/kiaf485
  • Primary Citation of Related Structures:  
    9RJ1

  • PubMed Abstract: 

    The nutritionally essential sulfur amino acids, methionine and cysteine, are present at suboptimal levels in legumes, such as common bean (Phaseolus vulgaris L.). β-Substituted alanine synthase 4;1 (BSAS4;1) is the major isoform of cytosolic cysteine synthase present in the developing seeds of common bean. There is evidence that in addition to cysteine, this enzyme is also involved in the biosynthesis of the non-proteinogenic amino acid S-methylcysteine, which accumulates in the form of a γ-glutamyl dipeptide. Here, we report the high-resolution structure of recombinant BSAS4;1. Unexpectedly, the crystal structure showed the presence of a molecule of benzoic acid near the active site, which appeared to have been co-purified from Escherichia coli. Kinetic analysis indicated that benzoic acid acts as a competitive inhibitor of BSAS4;1 with respect to O-acetylserine. IC50 values for benzoic acid and the structurally related salicylic acid were both equal to 0.6 mm. Using developing cotyledons grown in vitro, quantification of the incorporation of 13C3- and 15N-labeled serine into cysteine and downstream metabolites indicated that benzoic acid effectively inhibited cysteine biosynthesis in vivo at a concentration of 1.2 mm. The results of experiments tracking the incorporation of 13C-labeled sodium thiomethoxide provided further evidence that BSAS4;1 may be involved in the formation of free S-methylcysteine, through the condensation of O-acetylserine with methanethiol.


  • Organizational Affiliation
    • Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada, N5V 4T3.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine synthase324Phaseolus vulgarisMutation(s): 0 
Gene Names: PHAVU_007G185200g
EC: 2.5.1.47
UniProt
Find proteins for V7BIJ9 (Phaseolus vulgaris)
Explore V7BIJ9 
Go to UniProtKB:  V7BIJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV7BIJ9
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: 1.60 Å
  • R-Value Free:  0.168 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.141 (Depositor), 0.143 (DCC) 
  • R-Value Observed: 0.142 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.185α = 90
b = 69.185β = 90
c = 186.433γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release