6MRE | pdb_00006mre

E. coli cysteine desulfurase SufS R92A with a cysteine persulfide intermediate

• PDB DOI: https://doi.org/10.2210/pdb6MRE/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-10-12 Released: 2019-01-09 
• Deposition Author(s): Dunkle, J.A., Frantom, P.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.199 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Structural Evidence for Dimer-Interface-Driven Regulation of the Type II Cysteine Desulfurase, SufS.

Dunkle, J.A., Bruno, M.R., Outten, F.W., Frantom, P.A.

(2019) Biochemistry 58: 687-696

• PubMed: 30571100 
• DOI: https://doi.org/10.1021/acs.biochem.8b01122
• Primary Citation Related Structures: 
  6MR2, 6MR6, 6MRE, 6MRH, 6MRI


• PubMed Abstract: 
  

  SufS is a type II cysteine desulfurase and acts as the initial step in the Suf Fe-S cluster assembly pathway. In Escherichia coli, this pathway is utilized under conditions of oxidative stress and is resistant to reactive oxygen species. Mechanistically, this means SufS must shift between protecting a covalent persulfide intermediate and making it available for transfer to the next protein partner in the pathway, SufE. Here, we report five X-ray crystal structures of SufS including a new structure of SufS containing an inward-facing persulfide intermediate on C364. Additional structures of SufS variants with substitutions at the dimer interface show changes in dimer geometry and suggest a conserved β-hairpin structure plays a role in mediating interactions with SufE. These new structures, along with previous HDX-MS and biochemical data, identify an interaction network capable of communication between active-sites of the SufS dimer coordinating the shift between desulfurase and transpersulfurase activities.

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Organizational Affiliation: 
• Department of Chemistry & Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487 , United States.
Department of Chemistry & Biochemistry , The University of South Carolina , Columbia , South Carolina 29208 , United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.06 kDa 
• Atom Count: 3,270 
• Modeled Residue Count: 405 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase	A	420	Escherichia coli K-12	Mutation(s): 1  Gene Names: sufS, csdB, ynhB, b1680, JW1670 EC: 2.8.1.7 (PDB Primary Data), 4.4.1.16 (PDB Primary Data), 3.13.1 (UniProt)
UniProt
Find proteins for P77444 (Escherichia coli (strain K12)) Explore P77444  Go to UniProtKB:  P77444

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.199 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.98	α = 90
b = 126.98	β = 90
c = 135.22	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-09 
Deposition Author(s): Dunkle, J.A., Frantom, P.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM112919

Revision History  

• Version 1.0: 2019-01-09
  Type: Initial release
  
• Version 1.1: 2019-02-27
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection