7KQ4

Structure of isethionate sulfite-lyase from Bilophila wadsworthia with glycerol bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


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Literature

Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase.

Dawson, C.D.Irwin, S.M.Backman, L.R.F.Le, C.Wang, J.X.Vennelakanti, V.Yang, Z.Kulik, H.J.Drennan, C.L.Balskus, E.P.

(2021) Cell Chem Biol 

  • DOI: 10.1016/j.chembiol.2021.03.001
  • Primary Citation of Related Structures:  
    7KQ3, 7KQ4

  • PubMed Abstract: 
  • Desulfonation of isethionate by the bacterial glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslA) generates sulfite, a substrate for respiration that in turn produces the disease-associated metabolite hydrogen sulfide. Here, we present a 2.7 Å resolution X-ray structure of wild-type IslA from Bilophila wadsworthia with isethionate bound ...

    Desulfonation of isethionate by the bacterial glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslA) generates sulfite, a substrate for respiration that in turn produces the disease-associated metabolite hydrogen sulfide. Here, we present a 2.7 Å resolution X-ray structure of wild-type IslA from Bilophila wadsworthia with isethionate bound. In comparison with other GREs, alternate positioning of the active site β strands allows for distinct residue positions to contribute to substrate binding. These structural differences, combined with sequence variations, create a highly tailored active site for the binding of the negatively charged isethionate substrate. Through the kinetic analysis of 14 IslA variants and computational analyses, we probe the mechanism by which radical chemistry is used for C-S bond cleavage. This work further elucidates the structural basis of chemistry within the GRE superfamily and will inform structure-based inhibitor design of IsIA and thus of microbial hydrogen sulfide production.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02139, USA. Electronic address: balskus@chemistry.harvard.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isethionate sulfite-lyase AB830Bilophila wadsworthia 3_1_6Mutation(s): 0 
Gene Names: islAiseGHMPREF0179_00639
EC: 4.4.1
Find proteins for E5Y378 (Bilophila wadsworthia (strain 3_1_6))
Explore E5Y378 
Go to UniProtKB:  E5Y378
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.064α = 90
b = 132.962β = 90
c = 107.934γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

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 StatesR35 GM126982
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM069857

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release