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Structure of IDP04643

Crystal Structure of Phosphoribosylaminoimidazole Synthetase from Francisella tularensis

Edit deposit information
CSGID target
IDP04643 
PDB Id
3M84 (NCBI MMDB
Authors
N.Maltseva,Y.Kim,J.Hasseman,W.F.Anderson,A.Joachimiak 
Responsible person
Natalia Maltseva 
Responsible lab
Argonne National Laboratory 
Deposition Date
Mar 17, 2010 
Release Date
Jul 14, 2010 

Annotation

Description
Phosphoribosylaminoimidazole synthetase is the fifth enzyme in the de novo synthesis of purine nucleotides. It catalyzes the reaction to form 5-aminoimidizole ribonucleotide (AIR) from formylglycinamidine-ribonucleotide FGAM. This reaction closes the ring and produces a 5-membered imidazole ring of the purine nucleus (AIR). AIR synthetase catalyzes the transfer of the oxygen of the formyl group to phosphate. It is a sequential mechanism in which ATP binds first to the enzyme and ADP is released last. This enzyme hydrolyzes ATP to activate the oxygen of the amide in order to carry out a nucleophilic attack by nitrogen. Crystal Structure of Phosphoribosylaminoimidazole Synthetase from Francisella tularensis was solved at 1.7A in the presence of ADP. Overall structure represents dimer, each monomer consisting of three domains, the N-terminal alpha-beta domain, the small alpha-beta domain, and the small alpha domain. The N-terminal large alpha-beta domain interacts with the N-terminal domain of the other monomer using 4-stranded beta-sheet. In the structure, the ADP is processed to AMP and found in the patch between alpha-helices and the beta-sheet within in the N-terminal domain near the dimer interface formed by two beta-sheets. The active site is proposed to be the groove between the two beta-sheets from the two monomers. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
SO4
AMP
ACY
FMT
TRS Tris(hydroxymethyl)aminomethane
MSE modified residue

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=62.71Å, b=90.56Å, c=118.99Å
α=90.00, β=90.00, γ=90.00 
Solvent content
43.57  
Matthews coefficient
2.18  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
28.75-1.70Å (1.76-1.70Å)  
Rall(%)
15.5 
Rwork(%)
15.4 (17.2) 
Rfree(%)
18.3 (21.5) 
Num. observed reflections
76345 (5778) 
Num. Rfree reflections
3855 (301) 
Completeness(%)
96.5 (78.0) 

Model parameters

Num Atoms
6757  
Num Waters
816  
Num Hetatoms
0  
Model mean isotropic B factor
22.960Å2  
RMSD bond length
0.009Å  
RMSD bond angle
1.208°  
RMSD dihedral angle
18.004°
 
Filename uploaded
dep1w.pdb (uploaded on Mar 17, 2010 4:16 PM)  
Inserted
Mar 17, 2010