4U5R

Crystal structure of D106A mutant of RhCC (YP_702633.1) from Rhodococcus jostii RHA1 at 1.55 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


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Literature

Functional and structural characterization of an unusual cofactor-independent oxygenase.

Baas, B.J.Poddar, H.Geertsema, E.M.Rozeboom, H.J.de Vries, M.P.Permentier, H.P.Thunnissen, A.M.Poelarends, G.J.

(2015) Biochemistry 54: 1219-1232

  • DOI: 10.1021/bi501200j
  • Primary Citation of Related Structures:  
    4U5P, 4U5R

  • PubMed Abstract: 
  • The vast majority of characterized oxygenases use bound cofactors to activate molecular oxygen to carry out oxidation chemistry. Here, we show that an enzyme of unknown activity, RhCC from Rhodococcus jostii RHA1, functions as an oxygenase, using 4-hydroxyphenylenolpyruvate as a substrate ...

    The vast majority of characterized oxygenases use bound cofactors to activate molecular oxygen to carry out oxidation chemistry. Here, we show that an enzyme of unknown activity, RhCC from Rhodococcus jostii RHA1, functions as an oxygenase, using 4-hydroxyphenylenolpyruvate as a substrate. This unique and complex reaction yields 3-hydroxy-3-(4-hydroxyphenyl)-pyruvate, 4-hydroxybenzaldehyde, and oxalic acid as major products. Incubations with H2(18)O, (18)O2, and a substrate analogue suggest that this enzymatic oxygenation reaction likely involves a peroxide anion intermediate. Analysis of sequence similarity and the crystal structure of RhCC (solved at 1.78 Å resolution) reveal that this enzyme belongs to the tautomerase superfamily. Members of this superfamily typically catalyze tautomerization, dehalogenation, or decarboxylation reactions rather than oxygenation reactions. The structure shows the absence of cofactors, establishing RhCC as a rare example of a redox-metal- and coenzyme-free oxygenase. This sets the stage to study the mechanistic details of cofactor-independent oxygen activation in the unusual context of the tautomerase superfamily.


    Organizational Affiliation

    Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy and ‡Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RhCCA, B, C152Rhodococcus jostii RHA1Mutation(s): 1 
Gene Names: RHA1_ro02670
Find proteins for Q0SDB1 (Rhodococcus jostii (strain RHA1))
Explore Q0SDB1 
Go to UniProtKB:  Q0SDB1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
D [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.795α = 90
b = 57.784β = 90.41
c = 92.026γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific ResearchNetherlandsVIDI grant 700.56.421
European Research Coucil242293

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release