5ZSK

SufS from Bacillus subtilis soaked with L-cysteine for 63 sec


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Snapshots of PLP-substrate and PLP-product external aldimines as intermediates in two types of cysteine desulfurase enzymes.

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

(2020) FEBS J 287: 1138-1154

  • DOI: https://doi.org/10.1111/febs.15081
  • Primary Citation of Related Structures:  
    5WT2, 5WT4, 5ZS9, 5ZSK, 5ZSO, 5ZSP, 5ZST, 6KFZ, 6KG0, 6KG1

  • PubMed Abstract: 

    Cysteine desulfurase enzymes catalyze sulfur mobilization from l-cysteine to sulfur-containing biomolecules such as iron-sulfur (Fe-S) clusters and thio-tRNAs. The enzymes utilize the cofactor pyridoxal-5'-phosphate (PLP), which forms the external substrate- and product-aldimines and ketimines during catalysis and are grouped into two types (I and II) based on their different catalytic loops. To clarify the structure-based catalytic mechanisms for each group, we determined the structures of the external substrate- and product-aldimines as catalytic intermediates of NifS (type I) and SufS (type II) that are involved in Fe-S cluster biosynthesis using X-ray crystallographic snapshot analysis. As a common intermediate structure, the thiol group of the PLP-l-cysteine external aldimine is stabilized by the conserved histidine adjacent to PLP through a polar interaction. This interaction makes the thiol group orientated for subsequent nucleophilic attack by a conserved cysteine residue on the catalytic loop in the state of PLP-l-cysteine ketimine, which is formed from the PLP-l-cysteine aldimine. Unlike the intermediates, structural changes of the loops were different between the type I and II enzymes. In the type I enzyme, conformational and topological change of the loop is necessary for nucleophilic attack by the cysteine. In contrast, the loop in type II cysteine desulfurase enzymes showed no large conformational change; rather, it might possibly orient the thiol group of the catalytic cysteine for nucleophilic attack toward PLP-l-cysteine. The present structures allow a revision of the catalytic mechanism and may provide a clue for consideration of enzyme function, structural diversity, and evolution of cysteine desulfurase enzymes. DATABASE: Structural data are available in PDB database under the accession numbers 5WT2, 5WT4, 5ZSP, 5ZST, 5ZS9, 5ZSK, 5ZSO, 6KFZ, 6KG0, and 6KG1.


  • Organizational Affiliation

    Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PDA
Query on PDA

Download Ideal Coordinates CCD File 
B [auth A]2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID
C11 H17 N2 O7 P
WACJCHFWJNNBPR-ZETCQYMHSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSS
Query on CSS
A
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.8α = 90
b = 91.8β = 90
c = 127.5γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
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 ScienceJapan17K14510
Japan Society for the Promotion of ScienceJapan15H04472

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.3: 2020-04-01
    Changes: Database references
  • Version 1.4: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description