4UBG

Resting state of rat cysteine dioxygenase C93G variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The Cys-Tyr Cross-Link of Cysteine Dioxygenase Changes the Optimal pH of the Reaction without a Structural Change.

Davies, C.G.Fellner, M.Tchesnokov, E.P.Wilbanks, S.M.Jameson, G.N.

(2014) Biochemistry 53: 7961-7968

  • DOI: 10.1021/bi501277a
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cysteine dioxygenase (CDO) is a non-heme monoiron enzyme with an unusual posttranslational modification in the proximity of the ferrous iron active site. This modification, a cysteine to tyrosine thioether bond, cross-links two β-strands of the β-bar ...

    Cysteine dioxygenase (CDO) is a non-heme monoiron enzyme with an unusual posttranslational modification in the proximity of the ferrous iron active site. This modification, a cysteine to tyrosine thioether bond, cross-links two β-strands of the β-barrel. We have investigated its role in catalysis through a combined crystallographic and kinetic approach. The C93G variant lacks the cross-link and shows little change in structure from that of the wild type, suggesting that the cross-link does not stabilize an otherwise unfavorable conformation. A pH-dependent kinetic study shows that both cross-linked and un-cross-linked CDO are active but the optimal pH decreases with the presence of the cross-link. This result reflects the effect of the thioether bond on the pKa of Y157 and this residue's role in catalysis. At higher pH values, kcat is also higher for the cross-linked form, extending the pH range of activity. We therefore propose that the cross-link also increases activity by controlling deleterious interactions involving the thiol/ate of C93.


    Organizational Affiliation

    Department of Chemistry and MacDiarmid Institute for Advanced Materials and Nanotechnology and ‡Department of Biochemistry, University of Otago , P.O. Box 56, Dunedin 9054, New Zealand.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cysteine dioxygenase type 1
A
210Rattus norvegicusMutation(s): 1 
Gene Names: Cdo1
EC: 1.13.11.20
Find proteins for P21816 (Rattus norvegicus)
Go to UniProtKB:  P21816
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE2
Query on FE2

Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.202 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.84α = 90
b = 57.84β = 90
c = 122.73γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references
  • Version 1.2: 2014-12-17
    Changes: Database references
  • Version 1.3: 2015-01-14
    Changes: Database references
  • Version 1.4: 2015-02-04
    Changes: Derived calculations
  • Version 1.5: 2017-11-22
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy