1BRW

THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION

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 

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This is version 1.2 of the entry. See complete history. 


Literature

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

Pugmire, M.J., Ealick, S.E.

(1998) Structure 6: 1467-1479

  • DOI: 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) ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE)A, B433Geobacillus stearothermophilusMutation(s): 0 
Gene Names: pdp, pyn
EC: 2.4.2.2
UniProt
Find proteins for P77836 (Geobacillus stearothermophilus)
Explore P77836 
Go to UniProtKB:  P77836
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES
Download Ideal Coordinates CCD File 
 E [auth A], I [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
URA
Query on URA
Download Ideal Coordinates CCD File 
 H [auth B]URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
 C [auth A], F [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
 D [auth A], G [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
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 = 53.57α = 90
b = 70.45β = 98.02
c = 122.78γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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