5WAN

Crystal Structure of a flavoenzyme RutA in the pyrimidine catabolic pathway


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

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Literature

Catalysis of a flavoenzyme-mediated amide hydrolysis.

Mukherjee, T.Zhang, Y.Abdelwahed, S.Ealick, S.E.Begley, T.P.

(2010) J Am Chem Soc 132: 5550-1

  • DOI: 10.1021/ja9107676
  • Primary Citation of Related Structures:  
    5WAN

  • PubMed Abstract: 
  • A new pyrimidine catabolic pathway (the Rut pathway) was recently discovered in Escherichia coli K12. In this pathway, uracil is converted to 3-hydroxypropionate, ammonia, and carbon dioxide. The seven-gene Rut operon is required for this conversion. Here we demonstrate that the flavoenzyme RutA catalyzes the initial uracil ring-opening reaction to give 3-ureidoacrylate ...

    A new pyrimidine catabolic pathway (the Rut pathway) was recently discovered in Escherichia coli K12. In this pathway, uracil is converted to 3-hydroxypropionate, ammonia, and carbon dioxide. The seven-gene Rut operon is required for this conversion. Here we demonstrate that the flavoenzyme RutA catalyzes the initial uracil ring-opening reaction to give 3-ureidoacrylate. This reaction, while formally a hydrolysis reaction, proceeds by an oxidative mechanism initiated by the addition of a flavin hydroperoxide to the C4 carbonyl. While peroxide-catalyzed amide hydrolysis has chemical precedent, we are not aware of a prior example of analogous chemistry catalyzed by flavin hydroperoxides. This study further illustrates the extraordinary catalytic versatility of the flavin cofactor.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyrimidine monooxygenase RutAA403Escherichia coliMutation(s): 0 
Gene Names: rutABUE81_22975BW690_24255
EC: 1.14.99.46
UniProt
Find proteins for P75898 (Escherichia coli (strain K12))
Explore P75898 
Go to UniProtKB:  P75898
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP75898
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.85α = 90
b = 87.85β = 90
c = 96.368γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
MrBUMPphasing
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-19
    Type: Initial release