6CDN | pdb_00006cdn

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 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1038/s41589-018-0085-5
  • Primary Citation Related Structures: 
    6BGF, 6BGM, 6BPS, 6BPT, 6BPU, 6BPV, 6BPW, 6BPX, 6CDH, 6CDN

  • 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. 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.

Macromolecule Content 

  • Total Structure Weight: 23.63 kDa 
  • Atom Count: 1,688 
  • Modeled Residue Count: 186 
  • Deposited Residue Count: 200 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cysteine dioxygenase type 1200Homo 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
GTEx:  ENSG00000129596 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16878
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYS
(Subject of Investigation/LOI)

Query on CYS



Download:Ideal Coordinates CCD File
B [auth A]CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2
(Subject of Investigation/LOI)

Query on FE2



Download:Ideal Coordinates CCD File
C [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
3CT
Query on 3CT
A
L-PEPTIDE LINKINGC9 H10 Cl N O3TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free:  0.193 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
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


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
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description