1BRW

THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION

• PDB DOI:  https://doi.org/10.2210/pdb1BRW/pdb

• Classification: TRANSFERASE
• Organism(s): Geobacillus stearothermophilus
• Mutation(s): No 


• Deposited: 1998-08-25 Released: 1999-01-13 
• Deposition Author(s): Pugmire, M.J., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.276 
• R-Value Work: 0.232 
• R-Value Observed: 0.232 

Literature

The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation.

Pugmire, M.J., Ealick, S.E.

(1998) Structure 6: 1467-1479

• PubMed: 9817849 
• DOI: https://doi.org/10.1016/s0969-2126(98)00145-2
• Primary Citation of Related Structures:  
  1BRW


• PubMed Abstract: 
  

  Pyrimidine nucleoside phosphorylase (PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. In lower organisms (e.g. Bacillus stearothermophilus) PYNP accepts both thymidine and uridine, whereas in mammalian and other higher organisms it is specific for thymidine (designated thymidine phosphorylase, TP). PYNP shares 40% sequence similarity (and presumably significant structural similarity) with human TP, which has been implicated as a growth factor in tumor angiogenesis. It is thought that TP undergoes a major conformational change upon substrate binding that consequently produces an active conformation.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology Cornell University Ithaca NY 14853, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 92.9 kDa 
• Atom Count: 6,592 
• Modelled Residue Count: 866 
• Deposited Residue Count: 866 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE)	A, B	433	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: pdp, pyn EC: 2.4.2.2
UniProt
Find proteins for P77836 (Geobacillus stearothermophilus) Explore P77836  Go to UniProtKB:  P77836

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	E [auth A], I [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
URA	H [auth B]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N
PO4	C [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA	D [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.276 
• R-Value Work: 0.232 
• R-Value Observed: 0.232 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.57	α = 90
b = 70.45	β = 98.02
c = 122.78	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-01-13 
Deposition Author(s): Pugmire, M.J., Ealick, S.E.

Revision History  

• Version 1.0: 1999-01-13
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description