2I4T

Crystal structure of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with Imm-A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Inhibition and structure of Trichomonas vaginalis purine nucleoside phosphorylase with picomolar transition state analogues.

Rinaldo-Matthis, A.Wing, C.Ghanem, M.Deng, H.Wu, P.Gupta, A.Tyler, P.C.Evans, G.B.Furneaux, R.H.Almo, S.C.Wang, C.C.Schramm, V.L.

(2007) Biochemistry 46: 659-668

  • DOI: 10.1021/bi061515r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Trichomonas vaginalis is a parasitic protozoan purine auxotroph possessing a unique purine salvage pathway consisting of a bacterial type purine nucleoside phosphorylase (PNP) and a purine nucleoside kinase. Thus, T. vaginalis PNP (TvPNP) functions i ...

    Trichomonas vaginalis is a parasitic protozoan purine auxotroph possessing a unique purine salvage pathway consisting of a bacterial type purine nucleoside phosphorylase (PNP) and a purine nucleoside kinase. Thus, T. vaginalis PNP (TvPNP) functions in the reverse direction relative to the PNPs in other organisms. Immucillin-A (ImmA) and DADMe-Immucillin-A (DADMe-ImmA) are transition state mimics of adenosine with geometric and electrostatic features that resemble early and late transition states of adenosine at the transition state stabilized by TvPNP. ImmA demonstrates slow-onset tight-binding inhibition with TvPNP, to give an equilibrium dissociation constant of 87 pM, an inhibitor release half-time of 17.2 min, and a Km/Kd ratio of 70,100. DADMe-ImmA resembles a late ribooxacarbenium ion transition state for TvPNP to give a dissociation constant of 30 pM, an inhibitor release half-time of 64 min, and a Km/Kd ratio of 203,300. The tight binding of DADMe-ImmA supports a late SN1 transition state. Despite their tight binding to TvPNP, ImmA and DADMe-ImmA are weak inhibitors of human and P. falciparum PNPs. The crystal structures of the TvPNP x ImmA x PO4 and TvPNP x DADMe-ImmA x PO4 ternary complexes differ from previous structures with substrate analogues. The tight binding with DADMe-ImmA is in part due to a 2.7 A ionic interaction between a PO4 oxygen and the N1' cation of the hydroxypyrrolidine and is weaker in the TvPNP x ImmA x PO4 structure at 3.5 A. However, the TvPNP x ImmA x PO4 structure includes hydrogen bonds between the 2'-hydroxyl and the protein that are not present in TvPNP x DADMe-ImmA x PO4. These structures explain why DADMe-ImmA binds tighter than ImmA. Immucillin-H is a 12 nM inhibitor of TvPNP but a 56 pM inhibitor of human PNP. And this difference is explained by isotope-edited difference infrared spectroscopy with [6-18O]ImmH to establish that O6 is the keto tautomer in TvPNP x ImmH x PO4, causing an unfavorable leaving-group interaction.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trichomonas vaginalis purine nucleoside phosphorylase
A, B, C
236Trichomonas vaginalisMutation(s): 0 
Find proteins for A2E7Y6 (Trichomonas vaginalis)
Go to UniProtKB:  A2E7Y6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
UA2
Query on UA2

Download SDF File 
Download CCD File 
A, B, C
3,4-PYRROLIDINEDIOL,2-(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)-2S,3S,4R,5R
C11 H15 N5 O3
AMFDITJFBUXZQN-KUBHLMPHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UA2Ki: 1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.170 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 155.765α = 90.00
b = 155.765β = 90.00
c = 102.612γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-02-01
    Type: Structure summary
  • Version 1.4: 2017-10-18
    Type: Refinement description