8VBS | pdb_00008vbs

E. coli cysteine desulfurase SufS bound to SufE C51A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 
    0.272 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The structure of the SufS-SufE complex reveals interactions driving protected persulfide transfer in iron-sulfur cluster biogenesis.

Gogar, R.K.Chhikara, N.Vo, M.Gilbert, N.C.Dunkle, J.A.Frantom, P.A.

(2024) J Biological Chem 300: 107641-107641

  • DOI: https://doi.org/10.1016/j.jbc.2024.107641
  • Primary Citation of Related Structures:  
    8VBS

  • PubMed Abstract: 

    Fe-S clusters are critical cofactors for redox chemistry in all organisms. The cysteine desulfurase, SufS, provides sulfur in the SUF Fe-S cluster bioassembly pathway. SufS is a dimeric, pyridoxal 5'-phosphate-dependent enzyme that uses cysteine as a substrate to generate alanine and a covalent persulfide on an active site cysteine residue. SufS enzymes are activated by an accessory transpersulfurase protein, either SufE or SufU depending on the organism, which accepts the persulfide product and delivers it to downstream partners for Fe-S assembly. Here, using Escherichia coli proteins, we present the first X-ray crystal structure of a SufS/SufE complex. There is a 1:1 stoichiometry with each monomeric unit of the EcSufS dimer bound to one EcSufE subunit, though one EcSufE is rotated ∼7° closer to the EcSufS active site. EcSufE makes clear interactions with the α16 helix of EcSufS and site-directed mutants of several α16 residues were deficient in EcSufE binding. Analysis of the EcSufE structure showed a loss of electron density at the EcSufS/EcSufE interface for a flexible loop containing the highly conserved residue R119. An R119A EcSufE variant binds EcSufS but is not active in cysteine desulfurase assays and fails to support Fe-S cluster bioassembly in vivo. 35 S-transfer assays suggest that R119A EcSufE can receive a persulfide, suggesting the residue may function in a release mechanism. The structure of the EcSufS/EcSufE complex allows for comparison with other cysteine desulfurases to understand mechanisms of protected persulfide transfer across protein interfaces.


  • Organizational Affiliation
    • Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine desulfuraseA,
C [auth B]
406Escherichia coliMutation(s): 0 
Gene Names: sufS
EC: 2.8.1.7 (PDB Primary Data), 3.13.1 (UniProt), 4.4.1.16 (UniProt)
UniProt
Find proteins for P77444 (Escherichia coli (strain K12))
Explore P77444 
Go to UniProtKB:  P77444
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77444
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine desulfuration protein SufEB [auth C],
D
138Escherichia coliMutation(s): 2 
Gene Names: sufE
UniProt
Find proteins for P76194 (Escherichia coli (strain K12))
Explore P76194 
Go to UniProtKB:  P76194
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76194
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSS
Query on CSS
A,
C [auth B]
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
LLP
Query on LLP
A,
C [auth B]
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free:  0.272 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.492α = 90
b = 130.567β = 90
c = 101.185γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM142966
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM112919

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Database references