4R2X

Unique conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis uridine phosphorylase in the free form and in complex with uridine

• PDB DOI:  https://doi.org/10.2210/pdb4R2X/pdb
• Entry: 4R2X supersedes: 4HEN

• Classification: TRANSFERASE
• Organism(s): Shewanella oneidensis MR-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-13 Released: 2014-12-10 
• Deposition Author(s): Safonova, T.N., Mordkovich, N.N., Manuvera, V.A., Veiko, V.P., Popov, V.O., Polyakov, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.93 Å
• R-Value Free: 0.164 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 

Literature

High-syn conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis MR-1 uridine phosphorylase in the free form and in complex with uridine.

Safonova, T.N., Mikhailov, S.N., Veiko, V.P., Mordkovich, N.N., Manuvera, V.A., Alekseev, C.S., Kovalchuk, M.V., Popov, V.O., Polyakov, K.M.

(2014) Acta Crystallogr D Biol Crystallogr 70: 3310-3319

• PubMed: 25478848 
• DOI: https://doi.org/10.1107/S1399004714024079
• Primary Citation of Related Structures:  
  4R2W, 4R2X


• 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. Expression of UP from Shewanella oneidensis MR-1 (SoUP) was performed in Escherichia coli. The high-resolution X-ray structure of SoUP was solved in the free form and in complex with uridine. A crystal of SoUP in the free form was grown under microgravity and diffracted to ultrahigh resolution. Both forms of SoUP contained sulfate instead of phosphate in the active site owing to the presence of ammonium sulfate in the crystallization solution. The latter can be considered as a good mimic of phosphate. In the complex, uridine adopts a high-syn conformation with a nearly planar ribose ring and is present only in one subunit of the hexamer. A comparison of the structures of SoUP in the free form and in complex with the natural substrate uridine showed that the subunits of the hexamer are not identical, with the active sites having either an open or a closed conformation. In the monomers with the closed conformation, the active sites in which uridine is absent contain a glycerol molecule mimicking the ribose moiety of uridine.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 163.93 kDa 
• Atom Count: 12,369 
• Modelled Residue Count: 1,460 
• Deposited Residue Count: 1,512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uridine phosphorylase	A [auth C], B [auth D], C [auth E], D [auth F], E [auth A], F [auth B]	252	Shewanella oneidensis MR-1	Mutation(s): 0  Gene Names: udp, SO_4133 EC: 2.4.2.3
UniProt
Find proteins for Q8E9X9 (Shewanella oneidensis (strain MR-1)) Explore Q8E9X9  Go to UniProtKB:  Q8E9X9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	BA [auth A], G [auth C], GA [auth B], JA [auth B], M [auth D], R [auth E], T [auth E], W [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	AA [auth F], DA [auth A], EA [auth A], FA [auth A], HA [auth B], I [auth C], IA [auth B], J [auth C], K [auth C], KA [auth B], L [auth C], O [auth D], P [auth D], Q [auth D], S [auth E], U [auth E], V [auth E], Y [auth F], Z [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	CA [auth A], H [auth C], N [auth D], X [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.93 Å
• R-Value Free: 0.164 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.54	α = 90
b = 95.93	β = 120
c = 91.61	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Safonova, T.N., Mordkovich, N.N., Manuvera, V.A., Veiko, V.P., Popov, V.O., Polyakov, K.M.
• This entry supersedes: 4HEN

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2015-01-07
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description