7CET

Crystal structure of D-cycloserine-bound form of cysteine desulfurase NifS from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

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


Literature

Cycloserine enantiomers inhibit PLP-dependent cysteine desulfurase SufS via distinct mechanisms.

Nakamura, R.Ogawa, S.Takahashi, Y.Fujishiro, T.

(2022) FEBS J 

  • DOI: https://doi.org/10.1111/febs.16455
  • Primary Citation of Related Structures:  
    6KFY, 7CEO, 7CEP, 7CEQ, 7CER, 7CES, 7CET, 7CEU, 7E6A, 7E6B, 7E6C, 7E6D, 7E6E, 7E6F

  • PubMed Abstract: 

    The cysteine desulfurase SufS is a pyridoxal-5'-phosphate-dependent enzyme and is essential for the SUF system, which participates in iron-sulfur cluster biosynthesis. Inhibition of SufS in the SUF system by D-cycloserine (DCS) in Plasmodium falciparum apicoplast has recently been reported, indicating that SufS could be a target for malaria therapeutics. However, the mechanistic details underlying the inhibition of SufS by DCS have not yet been clarified. Moreover, inhibition of SufS by the other enantiomer, L-cycloserine (LCS), has not been investigated. Herein, we investigated the structure-based inhibition mechanisms of SufS by DCS and LCS using Bacillus subtilis SufS, whose catalytic mechanism has been well characterized in comparison to that of the P. falciparum SufS. Surprisingly, DCS- and LCS-mediated inhibitions of SufS occur via distinct mechanisms resulting in pyridoxamine-5'-phosphate (PMP) in DCS-mediated inhibition and PMP-3-hydroxyisoxazole adduct (PMP-isoxazole) in LCS-mediated inhibition. Biochemical and structural evaluation of SufS variants identified conserved His and Arg residues at the active site as the key determinants of the distinct inhibition mechanisms. The importance of structural elements involved in DCS and LCS-mediated inhibitions of SufS provides valuable insights for the structure-based design of new drugs targeting SufS. DATABASE: Structural data are available in PDB database under the accession numbers 6KFY, 7CEO, 7CEP, 7CEQ, 7CER, 7CES, 7CET, 7CEU, 7E6A, 7E6B, 7E6C, 7E6D, 7E6E, and 7E6F.


  • 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 IscS401Helicobacter pylori 26695Mutation(s): 2 
Gene Names: iscSHP_0220
EC: 2.8.1.7
UniProt
Find proteins for O25008 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25008 
Go to UniProtKB:  O25008
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25008
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.2α = 90
b = 103.2β = 90
c = 133.7γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan17K14510

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2022-04-27
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description