1Q1G

Crystal structure of Plasmodium falciparum PNP with 5'-methylthio-immucillin-H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Plasmodium falciparum Purine Nucleoside Phosphorylase: CRYSTAL STRUCTURES, IMMUCILLIN INHIBITORS, AND DUAL CATALYTIC FUNCTION.

Shi, W.Ting, L.M.Kicska, G.A.Lewandowicz, A.Tyler, P.C.Evans, G.B.Furneaux, R.H.Kim, K.Almo, S.C.Schramm, V.L.

(2004) J.Biol.Chem. 279: 18103-18106

  • DOI: 10.1074/jbc.C400068200
  • Primary Citation of Related Structures:  1NW4, 1RR6

  • PubMed Abstract: 
  • Purine nucleoside phosphorylase from Plasmodium falciparum (PfPNP) is an anti-malarial target based on the activity of Immucillins. The crystal structure of PfPNP.Immucillin-H (ImmH).SO(4) reveals a homohexamer with ImmH and SO(4) bound at each catal ...

    Purine nucleoside phosphorylase from Plasmodium falciparum (PfPNP) is an anti-malarial target based on the activity of Immucillins. The crystal structure of PfPNP.Immucillin-H (ImmH).SO(4) reveals a homohexamer with ImmH and SO(4) bound at each catalytic site. A solvent-filled cavity close to the 5'-hydroxyl group of ImmH suggested that PfPNP can accept additional functional groups at the 5'-carbon. Assays established 5'-methylthioinosine (MTI) as a substrate for PfPNP. MTI is not found in human metabolism. These properties of PfPNP suggest unusual purine pathways in P. falciparum and provide structural and mechanistic foundations for the design of malaria-specific transition state analogue inhibitors. 5'-Methylthio-Immucillin-H (MT-ImmH) was designed to resemble the transition state of PfPNP and binds to PfPNP and human-PNP with K(d) values of 2.7 and 303 nm, respectively, to give a discrimination factor of 112. MT-ImmH is the first inhibitor that favors PfPNP inhibition. The structure of PfPNP.MT-ImmH.SO(4) shows that the hydrophobic methylthio group inserts into a hydrophobic region adjacent to the more hydrophilic 5'-hydroxyl binding site of ImmH. The catalytic features of PfPNP indicate a dual cellular function in purine salvage and polyamine metabolism. Combined metabolic functions in a single enzyme strengthen the rationale for targeting PfPNP in anti-malarial action.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uridine phosphorylase putative
A, B, C, D, E, F
276Plasmodium falciparum (isolate 3D7)EC: 2.4.2.3
Find proteins for Q8I3X4 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I3X4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTI
Query on MTI

Download SDF File 
Download CCD File 
A, B, C, D, E, F
3,4-DIHYDROXY-2-[(METHYLSULFANYL)METHYL]-5-(4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)PYRROLIDINIUM
(1S)-1-(0-DEAZAHYPOXANTHIN-9-YL)-1,4-DIDEOXY-1,4-IMINO-5-METHYLTHIO-D-RIBITOL, MT-IMMUCILLIN-H, MT-IMMH
C12 H17 N4 O3 S
CEGIKIXYDFDYDN-RXDXJJGDSA-O
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A, B, D, E, F
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MTIKd: 2.7 nM BINDINGMOAD
MTIKd: 2.7 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.443α = 90.00
b = 91.733β = 90.00
c = 238.939γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance