RCSB PDB - 5V12: Crystal structure of Carbon Sulfoxide lyase, Egt2 Y134F with sulfenic acid intermediate

 5V12

Crystal structure of Carbon Sulfoxide lyase, Egt2 Y134F with sulfenic acid intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

Starting Model: experimental
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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 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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hercynylcysteine sulfoxide lyase501Neurospora crassa OR74AMutation(s): 0 
Gene Names: egt-2NCU11365
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
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hercynylcysteine sulfoxide lyaseE [auth C]501Neurospora crassa OR74AMutation(s): 0 
Gene Names: egt-2NCU11365
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8QJ
Query on 8QJ

Download Ideal Coordinates CCD File 
K [auth F],
P [auth A]
(1S)-1-carboxy-2-[2-(hydroxysulfanyl)-1H-imidazol-4-yl]-N,N,N-trimethylethan-1-aminium
C9 H16 N3 O3 S
ZLPHHLCGSBYNCO-ZETCQYMHSA-O
FMT
Query on FMT

Download Ideal Coordinates CCD File 
I [auth E]
J [auth G]
L [auth F]
M [auth H]
N [auth C]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A [auth E]
B [auth G]
C [auth F]
D [auth H]
F [auth D]
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
EXA
Query on EXA
E [auth C]PEPTIDE LINKINGC17 H27 N4 O9 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.021α = 90
b = 195.158β = 91.47
c = 110.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 8QJClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references, Structure summary
  • Version 2.0: 2023-10-04
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-11-15
    Changes: Data collection
  • Version 2.2: 2023-12-06
    Changes: Data collection
  • Version 3.0: 2024-05-01
    Changes: Derived calculations, Non-polymer description, Structure summary