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Structure of IDP90300

1.8 Angstrom resolution crystal structure of a putative deoxyribose-phosphate aldolase from Toxoplasma gondii ME49

Edit deposit information
CSGID target
IDP90300 
PDB Id
3QYQ (NCBI MMDB
Authors
A.S.Halavaty,J.Ruan,G.Minasov,L.Shuvalova,A.Ueno,M.Igarashi,H.Ngo,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Mar 03, 2011 
Release Date
Mar 30, 2011 

Annotation

Description
Toxoplasma gondii deoxyribose phosphate aldolase-like (TgDPA, TGME49_118750) gene expresses an essential bradyzoite-specific protein during its silent infection stage. Recently, TgDPA has been reported to interact with and enhance the activity of Toxoplasma actin depolymerizing factor (TgADF), implying it may be also involved in actin turnover, cyst maintenance and the inhibition of gliding motility of encysted bradyzoites. Study of the structural of TgDPA and its interaction with TgADF will shed new light on preventing tissue cyst formation and parasite re-emergence in immunocompromised patients. To gain a deeper understanding of this bradyzoite-specific protein, we have determined the crystal structure of the TgDPA(6-281) construct using molecular replacement phasing and refined to 1.8 Å resolution. The putative catalytic site of TgDPA was identified based on multiple sequence alignment with other known deoxyribose phosphate aldolases. A sucrose molecule, used in cryoprotection, is bound in the vicinity of that site. Each chain of TgDPA resembles (α8/β8)-TIM-barrel topology with an additional N-terminal α-helix, denoted the α0-helix. TgDPA forms a dimer in the crystal with an average buried surface area of 2,700.0 Å2. At the dimerization interface, helices α7 and α8 of two the monomers form a square-shaped opening, in which the α0-helices of the two monomers are inserted. This (α0/α7/α8)2-helical bundle creates a positively charged surface, which is exposed to the same solvent area as the N-termini of TgDPA beta-strands. This positively charged surface is proposed to be TgDPA’s interaction site with TgADF. The 40-Å long α6-helix of each chain in the dimer protrudes from the compact TIM-barrel structure into the solvent, and provides additional areas for the possible protein-protein interactions.  
Functional assignment
Lyase 

Ligands

Ligand code Name Ligand type
SUC crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 1  
Unit Cell

a=70.92Å, b=72.19Å, c=73.05Å
α=62.90, β=89.80, γ=88.85 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.49-1.80Å (1.85-1.80Å)  
Rall(%)
16.7 
Rwork(%)
16.6 (24.1) 
Rfree(%)
20.1 (26.6) 
Num. observed reflections
116431 (8155) 
Num. Rfree reflections
5821 (384) 
Completeness(%)
97.3 (92.4) 

Model parameters

Num Atoms
8833  
Num Waters
927  
Num Hetatoms
1107  
Model mean isotropic B factor
32.570Å2  
RMSD bond length
0.007Å  
RMSD bond angle
1.464°  
Filename uploaded
3QYQ.pdb (uploaded on Sep 28, 2011 11:07 AM)  
Inserted
Mar 23, 2011