8VIL

EgtB-IV from Crocosphaera subtropica, an ergothioneine-biosynthetic type IV sulfoxide synthase in complex with N,N-dimethyl-histidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


This is version 1.1 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 

  • DOI: https://doi.org/10.1016/j.str.2024.08.006
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AVI (Subject of Investigation/LOI)
Query on AVI

Download Ideal Coordinates CCD File 
G [auth A]N,N-dimethyl-L-histidine
C8 H13 N3 O2
IMOBSLOLPCWZKQ-ZETCQYMHSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
H [auth A],
L [auth B],
M [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE
Query on FE

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E [auth A],
K [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL

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C [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • 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

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Ligand Structure Quality Assessment 


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