Crystal structure of C212S mutant of Shewanella oneidensis MR-1 uridine phosphorylase

Experimental Data Snapshot

  • Resolution: 1.68 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

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Concerted action of two subunits of the functional dimer of Shewanella oneidensis MR-1 uridine phosphorylase derived from a comparison of the C212S mutant and the wild-type enzyme.

Safonova, T.N.Mordkovich, N.N.Veiko, V.P.Okorokova, N.A.Manuvera, V.A.Dorovatovskii, P.V.Popov, V.O.Polyakov, K.M.

(2016) Acta Crystallogr D Struct Biol 72: 203-210

  • DOI: https://doi.org/10.1107/S2059798315024353
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Uridine phosphorylase (UP; EC, a key enzyme in the pyrimidine-salvage pathway, catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. The structure of the C212S mutant of uridine phosphorylase from the facultatively aerobic Gram-negative γ-proteobacterium Shewanella oneidensis MR-1 (SoUP) was determined at 1.68 Å resolution. A comparison of the structures of the mutant and the wild-type enzyme showed that one dimer in the mutant hexamer differs from all other dimers in the mutant and wild-type SoUP (both in the free form and in complex with uridine). The key difference is the `maximum open' state of one of the subunits comprising this dimer, which has not been observed previously for uridine phosphorylases. Some conformational features of the SoUP dimer that provide access of the substrate into the active site are revealed. The binding of the substrate was shown to require the concerted action of two subunits of the dimer. The changes in the three-dimensional structure induced by the C212S mutation account for the lower affinity of the mutant for inorganic phosphate, while the affinity for uridine remains unchanged.

  • Organizational Affiliation

    Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridine phosphorylase252Shewanella oneidensis MR-1Mutation(s): 1 
Gene Names: udpSO_4133
Find proteins for Q8E9X9 (Shewanella oneidensis (strain MR-1))
Explore Q8E9X9 
Go to UniProtKB:  Q8E9X9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8E9X9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on URA

Download Ideal Coordinates CCD File 
G [auth D],
K [auth F],
M [auth A]
C4 H4 N2 O2
Query on SO4

Download Ideal Coordinates CCD File 
H [auth D]
I [auth D]
J [auth D]
L [auth F]
N [auth A]
H [auth D],
I [auth D],
J [auth D],
L [auth F],
N [auth A],
O [auth C],
P [auth E],
Q [auth E],
R [auth B]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.68 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.23α = 90
b = 95.4β = 119.98
c = 91.2γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation14-24-00172

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references
  • Version 1.2: 2016-03-02
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Database references
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description