6CDN

Crystal structure of cysteine-bound ferrous form of the crosslinked Cl-Tyr157 human cysteine dioxygenase

  • Classification: OXIDOREDUCTASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-02-08 Released: 2018-07-04 
  • Deposition Author(s): Liu, A., Li, J., Shin, I.
  • Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 

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This is version 1.4 of the entry. See complete history


Literature

Cleavage of a carbon-fluorine bond by an engineered cysteine dioxygenase.

Li, J.Griffith, W.P.Davis, I.Shin, I.Wang, J.Li, F.Wang, Y.Wherritt, D.J.Liu, A.

(2018) Nat Chem Biol 14: 853-860

  • DOI: 10.1038/s41589-018-0085-5
  • Primary Citation of Related Structures:  
    6CDH, 6CDN, 6BGM, 6BGF, 6BPU, 6BPT, 6BPW, 6BPV, 6BPX, 6BPS

  • PubMed Abstract: 
  • Cysteine dioxygenase (CDO) plays an essential role in sulfur metabolism by regulating homeostatic levels of cysteine. Human CDO contains a post-translationally generated Cys93-Tyr157 cross-linked cofactor. Here, we investigated this Cys-Tyr cross-linking by incorporating unnatural tyrosines in place of Tyr157 via a genetic method ...

    Cysteine dioxygenase (CDO) plays an essential role in sulfur metabolism by regulating homeostatic levels of cysteine. Human CDO contains a post-translationally generated Cys93-Tyr157 cross-linked cofactor. Here, we investigated this Cys-Tyr cross-linking by incorporating unnatural tyrosines in place of Tyr157 via a genetic method. The catalytically active variants were obtained with a thioether bond between Cys93 and the halogen-substituted Tyr157, and we determined the crystal structures of both wild-type and engineered CDO variants in the purely uncross-linked form and with a mature cofactor. Along with mass spectrometry and 19 F NMR, these data indicated that the enzyme could catalyze oxidative C-F or C-Cl bond cleavage, resulting in a substantial conformational change of both Cys93 and Tyr157 during cofactor assembly. These findings provide insights into the mechanism of Cys-Tyr cofactor biogenesis and may aid the development of bioinspired aromatic carbon-halogen bond activation.


    Organizational Affiliation

    Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, USA. Feradical@utsa.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cysteine dioxygenase type 1A200Homo sapiensMutation(s): 0 
Gene Names: CDO1
EC: 1.13.11.20
UniProt & NIH Common Fund Data Resources
Find proteins for Q16878 (Homo sapiens)
Explore Q16878 
Go to UniProtKB:  Q16878
PHAROS:  Q16878
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3CT
Query on 3CT
AL-PEPTIDE LINKINGC9 H10 Cl N O3TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.326α = 90
b = 131.326β = 90
c = 34.188γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-02-08 
  • Released Date: 2018-07-04 
  • Deposition Author(s): Liu, A., Li, J., Shin, I.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1623856
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM107529
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM108988

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence