7XEL | pdb_00007xel

SufS soaked with D-penicillamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Visualizing thiazolidine ring formation in the reaction of D-cysteine and pyridoxal-5'-phosphate within L-cysteine desulfurase SufS.

Nakamura, R.Fujishiro, T.

(2025) Biochem Biophys Res Commun 754: 151497-151497

  • DOI: https://doi.org/10.1016/j.bbrc.2025.151497
  • Primary Citation of Related Structures:  
    7XEJ, 7XEK, 7XEL, 7XEN, 7YB3

  • PubMed Abstract: 

    The reactivity of pyridoxal-5'-phosphate (PLP) with cysteine and its derivatives has been of increasing interest because the corresponding product, a thiazolidine PLP-cysteine adduct, can be formed via PLP-dependent enzymatic and non-enzymatic reactions. Here, we report biochemical and X-ray crystallographic snapshots of thiazolidine formation in reaction of D-cysteine with PLP in SufS, a PLP-dependent L-cysteine desulfurase. By comparing L- and D-penicillamine-bound SufS showing no thiazolidine formation in the crystals with D-cysteine SufS, we proposed a thiazolidine formation mechanism with important factors: the polar environments provided by the carbonyl groups of Ala28-Ala29 and Lys224-mediated base catalysis for the nucleophilic thiolate of D-cysteine.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine desulfurase SufS419Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: sufScsdyurWBSU32690
EC: 2.8.1.7
UniProt
Find proteins for O32164 (Bacillus subtilis (strain 168))
Explore O32164 
Go to UniProtKB:  O32164
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32164
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93α = 90
b = 93β = 90
c = 129γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan17K19340

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2025-04-02
    Changes: Database references, Structure summary