3BJE

Crystal structure of Trypanosoma brucei nucleoside phosphorylase shows uridine phosphorylase activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The Crystal Structure and Activity of a Putative Trypanosomal Nucleoside Phosphorylase Reveal It to be a Homodimeric Uridine Phosphorylase

Larson, E.T.Mudeppa, D.G.Gillespie, J.R.Mueller, N.Napuli, A.J.Arif, J.A.Ross, J.Arakaki, T.L.Lauricella, A.Detitta, G.Luft, J.Zucker, F.Verlinde, C.L.Fan, E.Van Voorhis, W.C.Buckner, F.S.Rathod, P.K.Hol, W.G.Merritt, E.A.

(2010) J Mol Biol 396: 1244-1259

  • DOI: 10.1016/j.jmb.2010.01.013
  • Primary Citation of Related Structures:  
    3BJE

  • PubMed Abstract: 
  • Purine nucleoside phosphorylases (PNPs) and uridine phosphorylases (UPs) are closely related enzymes involved in purine and pyrimidine salvage, respectively, which catalyze the removal of the ribosyl moiety from nucleosides so that the nucleotide base may be recycled ...

    Purine nucleoside phosphorylases (PNPs) and uridine phosphorylases (UPs) are closely related enzymes involved in purine and pyrimidine salvage, respectively, which catalyze the removal of the ribosyl moiety from nucleosides so that the nucleotide base may be recycled. Parasitic protozoa generally are incapable of de novo purine biosynthesis; hence, the purine salvage pathway is of potential therapeutic interest. Information about pyrimidine biosynthesis in these organisms is much more limited. Though all seem to carry at least a subset of enzymes from each pathway, the dependency on de novo pyrimidine synthesis versus salvage varies from organism to organism and even from one growth stage to another. We have structurally and biochemically characterized a putative nucleoside phosphorylase (NP) from the pathogenic protozoan Trypanosoma brucei and find that it is a homodimeric UP. This is the first characterization of a UP from a trypanosomal source despite this activity being observed decades ago. Although this gene was broadly annotated as a putative NP, it was widely inferred to be a purine nucleoside phosphorylase. Our characterization of this trypanosomal enzyme shows that it is possible to distinguish between PNP and UP activity at the sequence level based on the absence or presence of a characteristic UP-specificity insert. We suggest that this recognizable feature may aid in proper annotation of the substrate specificity of enzymes in the NP family.


    Organizational Affiliation

    Medical Structural Genomics of Pathogenic Protozoa Consortium, University of Washington, Seattle, WA 98195, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoside phosphorylase, putativeA, B349Trypanosoma bruceiMutation(s): 0 
Gene Names: Tb927.8.4430
EC: 2.4.2
Find proteins for Q57VZ2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q57VZ2 
Go to UniProtKB:  Q57VZ2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R1P
Query on R1P

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]1-O-phosphono-alpha-D-ribofuranose
C5 H11 O8 P
YXJDFQJKERBOBM-TXICZTDVSA-N
 Ligand Interaction
URA
Query on URA

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.015α = 90
b = 95.387β = 105.91
c = 63.483γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary