4YJK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1107/S2059798315024353

  • PubMed Abstract: 
  • Uridine phosphorylase (UP; EC 2.4.2.3), 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 facultati ...

    Uridine phosphorylase (UP; EC 2.4.2.3), 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uridine phosphorylase
D, F, A, C, E, B
252Shewanella oneidensis (strain MR-1)Mutation(s): 1 
Gene Names: udp
EC: 2.4.2.3
Find proteins for Q8E9X9 (Shewanella oneidensis (strain MR-1))
Go to UniProtKB:  Q8E9X9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
URA
Query on URA

Download SDF File 
Download CCD File 
A, D, F
URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.138 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 91.230α = 90.00
b = 95.400β = 119.98
c = 91.200γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation14-24-00172

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2016-02-10
    Type: Database references
  • Version 1.2: 2016-03-02
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Database references