4QM8

Crystal Structure of a Putative Cysteine Dioxygnase From Bacillus subtilis: A Alternative Modeling of 3EQE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:3EQE


Literature

Structures of Arg- and Gln-type bacterial cysteine dioxygenase homologs.

Driggers, C.M.Hartman, S.J.Karplus, P.A.

(2015) Protein Sci 24: 154-161

  • DOI: 10.1002/pro.2587
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In some bacteria, cysteine is converted to cysteine sulfinic acid by cysteine dioxygenases (CDO) that are only ∼15-30% identical in sequence to mammalian CDOs. Among bacterial proteins having this range of sequence similarity to mammalian CDO are som ...

    In some bacteria, cysteine is converted to cysteine sulfinic acid by cysteine dioxygenases (CDO) that are only ∼15-30% identical in sequence to mammalian CDOs. Among bacterial proteins having this range of sequence similarity to mammalian CDO are some that conserve an active site Arg residue ("Arg-type" enzymes) and some having a Gln substituted for this Arg ("Gln-type" enzymes). Here, we describe a structure from each of these enzyme types by analyzing structures originally solved by structural genomics groups but not published: a Bacillus subtilis "Arg-type" enzyme that has cysteine dioxygenase activity (BsCDO), and a Ralstonia eutropha "Gln-type" CDO homolog of uncharacterized activity (ReCDOhom). The BsCDO active site is well conserved with mammalian CDO, and a cysteine complex captured in the active site confirms that the cysteine binding mode is also similar. The ReCDOhom structure reveals a new active site Arg residue that is hydrogen bonding to an iron-bound diatomic molecule we have interpreted as dioxygen. Notably, the Arg position is not compatible with the mode of Cys binding seen in both rat CDO and BsCDO. As sequence alignments show that this newly discovered active site Arg is well conserved among "Gln-type" CDO enzymes, we conclude that the "Gln-type" CDO homologs are not authentic CDOs but will have substrate specificity more similar to 3-mercaptopropionate dioxygenases.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Bldg, Oregon State University, Corvallis, Oregon, 97331.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cysteine dioxygenaseA, B173Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: BSU31140cdoACysteine DioxygenaseyubC
EC: 1.13.11.20
Find proteins for O32085 (Bacillus subtilis (strain 168))
Explore O32085 
Go to UniProtKB:  O32085
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYS
Query on CYS

Download CCD File 
A, B
CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
 Ligand Interaction
FE
Query on FE

Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.83α = 90
b = 65.83β = 90
c = 197.19γ = 90
Software Package:
Software NamePurpose
SHELXDEphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-31
    Changes: Database references
  • Version 1.2: 2015-01-14
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Advisory, Refinement description