5UTS | pdb_00005uts

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 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5UTS

This is version 1.2 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: https://doi.org/10.1016/j.chembiol.2018.02.002
  • Primary Citation 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. 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 Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA.

Macromolecule Content 

  • Total Structure Weight: 455.99 kDa 
  • Atom Count: 28,997 
  • Modeled Residue Count: 3,513 
  • Deposited Residue Count: 4,008 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
C-S Lyase Egt2501Neurospora crassa OR74AMutation(s): 0 
Gene Names: egt-2NCU11365
EC: 4.4.1 (PDB Primary Data), 4.4.1.36 (UniProt)
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
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D 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 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
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



Entry History 

Deposition Data

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
  • Version 1.2: 2025-04-02
    Changes: Data collection, Database references, Structure summary