Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 556.16 kDa 
• Atom Count: 37086 
• Modelled Residue Count: 4487 
• Deposited Residue Count: 5076 
• Unique protein chains: 1

3QPB

Crystal Structure of Streptococcus Pyogenes Uridine Phosphorylase Reveals a Subclass of the NP-I Superfamily

• PDB DOI: 10.2210/pdb3QPB/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pyogenes serotype M6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-11 Released: 2011-08-24 
• Deposition Author(s): Tran, T.H., Christoffersen, S., Parker, W.B., Piskur, J., Serra, I., Terreni, M., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.203 
• R-Value Work: 0.177 

Literature

The Crystal Structure of Streptococcus pyogenes Uridine Phosphorylase Reveals a Distinct Subfamily of Nucleoside Phosphorylases.

Tran, T.H., Christoffersen, S., Allan, P.W., Parker, W.B., Serra, I., Terreni, M., Ealick, S.E.

(2011) Biochemistry 50: 6549-6558

• PubMed: 21707079 
• DOI: 10.1021/bi200707z
• Primary Citation of Related Structures:  
  3QPB


• PubMed Abstract: 
  

Uridine phosphorylase (UP), a key enzyme in the pyrimidine salvage pathway, catalyzes the reversible phosphorolysis of uridine or 2'-deoxyuridine to uracil and ribose 1-phosphate or 2'-deoxyribose 1-phosphate. This enzyme belongs to the nucleoside phosphorylase I superfamily whose members show diverse specificity for nucleoside substrates. Phylogenetic analysis shows Streptococcus pyogenes uridine phosphorylase (SpUP) is found in a distinct branch of the pyrimidine subfamily of nucleoside phosphorylases. To further characterize SpUP, we determined the crystal structure in complex with the products, ribose 1-phosphate and uracil, at 1.8 Å resolution. Like Escherichia coli UP (EcUP), the biological unit of SpUP is a hexamer with an α/β monomeric fold. A novel feature of the active site is the presence of His169, which structurally aligns with Arg168 of the EcUP structure. A second active site residue, Lys162, is not present in previously determined UP structures and interacts with O2 of uracil. Biochemical studies of wild-type SpUP showed that its substrate specificity is similar to that of EcUP, while EcUP is ∼7-fold more efficient than SpUP. Biochemical studies of SpUP mutants showed that mutations of His169 reduced activity, while mutation of Lys162 abolished all activity, suggesting that the negative charge in the transition state resides mostly on uracil O2. This is in contrast to EcUP for which transition state stabilization occurs mostly at O4.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	282	Streptococcus pyogenes serotype M6	Mutation(s): 0  Gene Names: M6_Spy1599 EC: 2.4.2.3
UniProt
Find proteins for Q5XA29 (Streptococcus pyogenes serotype M6 (strain ATCC BAA-946 / MGAS10394)) Explore Q5XA29  Go to UniProtKB:  Q5XA29

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R1P	AA [auth E], AB [auth R], CA [auth F], EA [auth G], GA [auth H], IA [auth I], KA [auth J], MA [auth K], OA [auth L], QA [auth M], S [auth A], SA [auth N], U [auth B], UA [auth O], W [auth C], WA [auth P], Y [auth D], YA [auth Q]	1-O-phosphono-alpha-D-ribofuranose C5 H11 O8 P YXJDFQJKERBOBM-TXICZTDVSA-N
URA	BA [auth E], BB [auth R], DA [auth F], FA [auth G], HA [auth H], JA [auth I], LA [auth J], NA [auth K], PA [auth L], RA [auth M], T [auth A], TA [auth N], V [auth B], VA [auth O], X [auth C], XA [auth P], Z [auth D], ZA [auth Q]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.203 
• R-Value Work: 0.177 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.021	α = 78.46
b = 91.578	β = 82.33
c = 170.18	γ = 60.12

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-02-11 
• Released Date: 2011-08-24 
Deposition Author(s): Tran, T.H., Christoffersen, S., Parker, W.B., Piskur, J., Serra, I., Terreni, M., Ealick, S.E.

Revision History  

• Version 1.0: 2011-08-24
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary