Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 187.45 kDa 
• Atom Count: 11,789 
• Modelled Residue Count: 1,458 
• Deposited Residue Count: 1,656 
• Unique protein chains: 1

 1Q1G

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

• PDB DOI: 10.2210/pdb1Q1G/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-07-19 Released: 2004-03-16 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.242 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 

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

• PubMed: 14982926 
• DOI: 10.1074/jbc.C400068200
• Primary Citation of Related Structures:  
  1NW4, 1Q1G, 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase putative	A, B, C, D, E, F	276	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PNP, PF3D7_0513300 EC: 2.4.2.1 (PDB Primary Data), 2.4.2.44 (UniProt)
UniProt
Find proteins for Q8I3X4 (Plasmodium falciparum (isolate 3D7)) Explore Q8I3X4  Go to UniProtKB:  Q8I3X4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTI	CA [auth D], IA [auth E], K [auth A], OA [auth F], Q [auth B], X [auth C]	3,4-DIHYDROXY-2-[(METHYLSULFANYL)METHYL]-5-(4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)PYRROLIDINIUM C12 H17 N4 O3 S CEGIKIXYDFDYDN-RXDXJJGDSA-O
SO4	AA [auth D], BA [auth D], FA [auth E], G [auth A], GA [auth E], H [auth A], HA [auth E], I [auth A], J [auth A], KA [auth F], LA [auth F], M [auth B], MA [auth F], N [auth B], NA [auth F], O [auth B], P [auth B], U [auth C], V [auth C], W [auth C], Y [auth D], Z [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
IPA	DA [auth D], EA [auth D], JA [auth E], L [auth A], PA [auth F], QA [auth F], R [auth B], S [auth B], T [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MTI	PDBBind:  1Q1G	Kd: 2.7 (nM) from 1 assay(s)
	Binding MOAD:  1Q1G	Kd: 2.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.242 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.443	α = 90
b = 91.733	β = 90
c = 238.939	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-16 
Deposition Author(s): 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.

Revision History  

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