1LX7 | pdb_00001lx7

Structure of E. coli uridine phosphorylase at 2.0A

• PDB DOI: https://doi.org/10.2210/pdb1LX7/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-06-04 Released: 2002-06-12 
• Deposition Author(s): Burling, T., Buglino, J.A., Kniewel, R., Chadna, T., Beckwith, A., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.215 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.184 (DCC) 

Literature

Structure of Escherichia coli uridine phosphorylase at 2.0 A.

Burling, F.T., Kniewel, R., Buglino, J.A., Chadha, T., Beckwith, A., Lima, C.D.

(2003) Acta Crystallogr D Biol Crystallogr 59: 73-76

• PubMed: 12499542 
• DOI: https://doi.org/10.1107/s0907444902018929
• Primary Citation Related Structures: 
  1LX7


• PubMed Abstract: 
  

  The 2.0 A crystal structure has been determined for Escherichia coli uridine phosphorylase (UP), an essential enzyme in nucleotide biosynthesis that catalyzes the phosphorolytic cleavage of the C-N glycosidic bond of uridine to ribose-1-phosphate and uracil. The structure determination of two independent monomers in the asymmetric unit revealed the residue composition and atomic details of the apo configurations of each active site. The native hexameric UP enzyme was revealed by applying threefold crystallographic symmetry to the contents of the asymmetric unit. The 2.0 A model reveals a closer structural relationship to other nucleotide phosphorylase enzymes than was previously appreciated.

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Organizational Affiliation: 
• Biochemistry Department and Structural Biology Program, Weill Medical College of Cornell University, New York, NY 10021, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 55.13 kDa 
• Atom Count: 3,873 
• Modeled Residue Count: 471 
• Deposited Residue Count: 506 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uridine phosphorylase	A, B	253	Escherichia coli	Mutation(s): 8  EC: 2.4.2.3
UniProt
Find proteins for P12758 (Escherichia coli (strain K12)) Explore P12758  Go to UniProtKB:  P12758

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.215 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.184 (DCC) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.375	α = 90
b = 151.375	β = 90
c = 48.151	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-12 
Deposition Author(s): Burling, T., Buglino, J.A., Kniewel, R., Chadna, T., Beckwith, A., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2002-06-12
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary