5UTS

Carbon Sulfoxide lyase, Egt2 in the Ergothioneine biosynthesis pathway

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Snapshots of C-S Cleavage in Egt2 Reveals Substrate Specificity and Reaction Mechanism.

Irani, S., Naowarojna, N., Tang, Y., Kathuria, K.R., Wang, S., Dhembi, A., Lee, N., Yan, W., Lyu, H., Costello, C.E., Liu, P., Zhang, Y.J.

(2018) Cell Chem Biol 25: 519-529.e4

  • DOI: 10.1016/j.chembiol.2018.02.002
  • Primary Citation of Related Structures:  
    5UTS, 5V12, 5V1X

  • PubMed Abstract: 

    • Sulfur incorporation in the biosynthesis of ergothioneine, a histidine thiol derivative, differs from other well-characterized transsulfurations. A combination of a mononuclear non-heme iron enzyme-catalyzed oxidative C-S bond formation and a subsequent pyridoxal 5'-phosphate (PLP)-mediated C-S lyase reaction leads to the net transfer of a sulfur atom from a cysteine to a histidine ...

    Sulfur incorporation in the biosynthesis of ergothioneine, a histidine thiol derivative, differs from other well-characterized transsulfurations. A combination of a mononuclear non-heme iron enzyme-catalyzed oxidative C-S bond formation and a subsequent pyridoxal 5'-phosphate (PLP)-mediated C-S lyase reaction leads to the net transfer of a sulfur atom from a cysteine to a histidine. In this study, we structurally and mechanistically characterized a PLP-dependent C-S lyase Egt2, which mediates the sulfoxide C-S bond cleavage in ergothioneine biosynthesis. A cation-π interaction between substrate and enzyme accounts for Egt2's preference of sulfoxide over thioether as a substrate. Using mutagenesis and structural biology, we captured three distinct states of the Egt2 C-S lyase reaction cycle, including a labile sulfenic intermediate captured in Egt2 crystals. Chemical trapping and high-resolution mass spectrometry were used to confirm the involvement of the sulfenic acid intermediate in Egt2 catalysis.

    Organizational Affiliation: 

    Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address: jzhang@cm.utexas.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-S Lyase Egt2501Neurospora crassa OR74AMutation(s): 0 
Gene Names: egt-2, NCU11365
EC: 4.4.1
UniProt
Find proteins for A7UX13 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
Explore A7UX13 
Go to UniProtKB:  A7UX13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7UX13
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A [auth G],
B [auth C],
C [auth H],
D,
E,
A [auth G],
B [auth C],
C [auth H],
D,
E,
F,
G [auth B],
H [auth A]
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
MSE
Query on MSE
A [auth G],
B [auth C],
C [auth H],
D,
E,
A [auth G],
B [auth C],
C [auth H],
D,
E,
F,
G [auth B],
H [auth A]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.84α = 90
b = 195.341β = 91.32
c = 107.791γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2017-02-15 
  • Released Date: 2018-02-21 
    • Deposition Author(s): Irani, S., Zhang, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references