2ISC

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

Summary for 2ISC

• Entry DOI: 10.2210/pdb2isc/pdb
• Related: 2I4T
• Descriptor: purine nucleoside phosphorylase, PHOSPHATE ION, (3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL, ... (4 entities in total)
• Functional Keywords: purine nucleoside phosphorylase, transferase
• Biological source: Trichomonas vaginalis
• Total number of polymer chains: 6
• Total formula weight: 160537.02

Authors

Rinaldo-Matthis, A.,Almo, S.C.,Schramm, V.L. (deposition date: 2006-10-17, release date: 2007-06-05, Last modification date: 2024-02-21)

Primary citation

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.
Inhibition and structure of Trichomonas vaginalis purine nucleoside phosphorylase with picomolar transition state analogues
Biochemistry, 46:659-668, 2007

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 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.

PubMed: 17223688
DOI: 10.1021/bi061515r

Experimental method

X-RAY DIFFRACTION (2.7 Å)