Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 92899.02 
• Atom Count: 6482 
• Residue Count: 866 
• Unique protein chains: 1

1BRW

THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION

• DOI: 10.2210/pdb1BRW/pdb

• Classification: TRANSFERASE
• Organism(s): Geobacillus stearothermophilus


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.276 
• R-Value Work: 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 


• 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.

---

Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.276 
• R-Value Work: 0.232 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 53.570	α = 90.00
b = 70.450	β = 98.02
c = 122.780	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-08-25 
• 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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance