3VC3 | pdb_00003vc3

Crystal structure of beta-cyanoalanine synthase K95A mutant in soybean


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.202 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

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Literature

Structure of Soybean beta-Cyanoalanine Synthase and the Molecular Basis for Cyanide Detoxification in Plants.

Yi, H.Juergens, M.Jez, J.M.

(2012) Plant Cell 24: 2696-2706

  • DOI: https://doi.org/10.1105/tpc.112.098954
  • Primary Citation Related Structures: 
    3VBE, 3VC3

  • PubMed Abstract: 

    Plants produce cyanide (CN-) during ethylene biosynthesis in the mitochondria and require β-cyanoalanine synthase (CAS) for CN- detoxification. Recent studies show that CAS is a member of the β-substituted alanine synthase (BSAS) family, which also includes the Cys biosynthesis enzyme O-acetylserine sulfhydrylase (OASS), but how the BSAS evolved distinct metabolic functions is not understood. Here we show that soybean (Glycine max) CAS and OASS form α-aminoacrylate reaction intermediates from Cys and O-acetylserine, respectively. To understand the molecular evolution of CAS and OASS in the BSAS enzyme family, the crystal structures of Gm-CAS and the Gm-CAS K95A mutant with a linked pyridoxal phosphate (PLP)-Cys molecule in the active site were determined. These structures establish a common fold for the plant BSAS family and reveal a substrate-induced conformational change that encloses the active site for catalysis. Comparison of CAS and OASS identified residues that covary in the PLP binding site. The Gm-OASS T81M, S181M, and T185S mutants altered the ratio of OASS:CAS activity but did not convert substrate preference to that of a CAS. Generation of a triple mutant Gm-OASS successfully switched reaction chemistry to that of a CAS. This study provides new molecular insight into the evolution of diverse enzyme functions across the BSAS family in plants.


  • Organizational Affiliation
    • Department of Biology, Washington University, St. Louis, Missouri 63130, USA.

Macromolecule Content 

  • Total Structure Weight: 225.18 kDa 
  • Atom Count: 16,613 
  • Modeled Residue Count: 1,934 
  • Deposited Residue Count: 2,064 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
beta-cyanoalnine synthase
A, B, C, D, E
A, B, C, D, E, F
344Glycine maxMutation(s): 0 
Gene Names: GLYMA09G39390OAS-TL3
EC: 2.5.1.47
UniProt
Find proteins for I1L6I6 (Glycine max)
Explore I1L6I6 
Go to UniProtKB:  I1L6I6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI1L6I6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.202 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.092α = 90
b = 154.325β = 90
c = 198.328γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations