1P9B

Structure of fully ligated Adenylosuccinate synthetase from Plasmodium falciparum

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 

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Literature

Crystal Structure of Fully Ligated Adenylosuccinate Synthetase from Plasmodium falciparum.

Eaazhisai, K., Jayalakshmi, R., Gayathri, P., Anand, R.P., Sumathy, K., Balaram, H., Murthy, M.R.

(2004) J Mol Biol 335: 1251-1264

  • DOI: 10.1016/j.jmb.2003.11.036
  • Primary Citation of Related Structures:  
    1P9B

  • PubMed Abstract: 

    • In the absence of the de novo purine nucleotide biosynthetic pathway in parasitic protozoa, purine salvage is of primary importance for parasite survival. Enzymes of the salvage pathway are, therefore, good targets for anti-parasitic drugs. Adenylosuccinate synthetase (AdSS), catalysing the first committed step in the synthesis of AMP from IMP, is a potential target for anti-protozoal chemotherapy ...

    In the absence of the de novo purine nucleotide biosynthetic pathway in parasitic protozoa, purine salvage is of primary importance for parasite survival. Enzymes of the salvage pathway are, therefore, good targets for anti-parasitic drugs. Adenylosuccinate synthetase (AdSS), catalysing the first committed step in the synthesis of AMP from IMP, is a potential target for anti-protozoal chemotherapy. We report here the crystal structure of adenylosuccinate synthetase from the malaria parasite, Plasmodium falciparum, complexed to 6-phosphoryl IMP, GDP, Mg2+ and the aspartate analogue, hadacidin at 2 A resolution. The overall architecture of P. falciparum AdSS (PfAdSS) is similar to the known structures from Escherichia coli, mouse and plants. Differences in substrate interactions seen in this structure provide a plausible explanation for the kinetic differences between PfAdSS and the enzyme from other species. Additional hydrogen bonding interactions of the protein with GDP may account for the ordered binding of substrates to the enzyme. The dimer interface of PfAdSS is also different, with a pronounced excess of positively charged residues. Differences highlighted here provide a basis for the design of species-specific inhibitors of the enzyme.

    Organizational Affiliation: 

    Molecular Biophysics Unit, UGC Centre of Advanced Study, Indian Institute of Science, Bangalore 560012, India.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenylosuccinate SynthetaseA442Plasmodium falciparumMutation(s): 0 
Gene Names: Adss
EC: 6.3.4.4
UniProt
Find proteins for Q9U8D3 (Plasmodium falciparum)
Explore Q9U8D3 
Go to UniProtKB:  Q9U8D3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9U8D3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
F [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
IMO
Query on IMO
Download Ideal Coordinates CCD File 
D [auth A]6-O-PHOSPHORYL INOSINE MONOPHOSPHATE
C10 H14 N4 O11 P2
RXRZOKQPANIEDW-KQYNXXCUSA-N		 Ligand Interaction
HDA
Query on HDA
Download Ideal Coordinates CCD File 
E [auth A]HADACIDIN
C3 H5 N O4
URJHVPKUWOUENU-UHFFFAOYSA-N		 Ligand Interaction
NO3
Query on NO3
Download Ideal Coordinates CCD File 
C [auth A]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.579α = 90
b = 117.117β = 90
c = 80.416γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-03
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance