8VIK | pdb_00008vik

EgtB-IV from Crocosphaera subtropica, a type IV sulfoxide synthase involved in ergothioneine biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.219 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural insights into the convergent evolution of sulfoxide synthase EgtB-IV, an ergothioneine-biosynthetic homolog of ovothiol synthase OvoA.

Ireland, K.A.Kayrouz, C.M.Abbott, M.L.Seyedsayamdost, M.R.Davis, K.M.

(2024) Structure 32: 2013-2022.e5

  • DOI: https://doi.org/10.1016/j.str.2024.08.006
  • Primary Citation Related Structures: 
    8VIG, 8VIH, 8VII, 8VIK, 8VIL

  • PubMed Abstract: 

    Non-heme iron-dependent sulfoxide/selenoxide synthases (NHISS) constitute a unique metalloenzyme class capable of installing a C-S/Se bond onto histidine to generate thio/selenoimidazole antioxidants, such as ergothioneine and ovothiol. These natural products are increasingly recognized for their health benefits. Among associated ergothioneine-biosynthetic enzymes, type IV EgtBs stand out, as they exhibit low sequence similarity with other EgtB subfamilies due to their recent divergence from the ovothiol-biosynthetic enzyme OvoA. Herein, we present crystal structures of two representative EgtB-IV enzymes, offering insights into the basis for this evolutionary convergence and enhancing our understanding of NHISS active site organization more broadly. The ability to interpret how key residues modulate substrate specificity and regioselectivity has implications for downstream identification of divergent reactivity within the NHISS family. To this end, we identify a previously unclassified clade of OvoA-like enzymes with a seemingly hybrid set of characteristics, suggesting they may represent an evolutionary intermediate between OvoA and EgtB-IV.


  • Organizational Affiliation
    • Department of Chemistry, Emory University, Atlanta, GA 30322, USA.

Macromolecule Content 

  • Total Structure Weight: 110.14 kDa 
  • Atom Count: 7,403 
  • Modeled Residue Count: 863 
  • Deposited Residue Count: 936 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sulfoxide synthase EgtB-IV
A, B
468Crocosphaera subtropica ATCC 51142Mutation(s): 0 
Gene Names: cce_1041
UniProt
Find proteins for B1WTS6 (Crocosphaera subtropica (strain ATCC 51142 / BH68))
Explore B1WTS6 
Go to UniProtKB:  B1WTS6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1WTS6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
K [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.219 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.197α = 90
b = 94.511β = 100.16
c = 83.747γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1937971
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM147557

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Database references, Structure summary