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Structure of IDP04643

Crystal Structure of Phosphoribosylaminoimidazole Synthetase fromFrancisella tularensis complexed with pyrophosphate.

Edit deposit information
CSGID target
IDP04643 
PDB Id
3QTY (NCBI MMDB
Authors
N.Maltseva,Y.Kim,J.Hasseman,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Natalia Maltseva 
Responsible lab
Argonne National Laboratory 
Deposition Date
Feb 23, 2011 
Release Date
Mar 16, 2011 

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 1.8A in the presence of pyrophosphate. 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. 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
TRS Tris(hydroxymethyl)aminomethane crystallization
POP pyrophosphate 2- crystallization
PO4 PHOSPHATE ION crystallization
SO4 crystallization
MSE modified residue
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=65.48Å, b=88.72Å, c=112.98Å
α=90.00, β=90.00, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
34.67-1.80Å (1.83-1.80Å)  
Rall(%)
17.0 
Rwork(%)
16.9 (23.4) 
Rfree(%)
20.2 (28.2) 
Num. observed reflections
64417 (2628) 
Num. Rfree reflections
3272 (111) 
Completeness(%)
99.4 (95.0) 

Model parameters

Num Atoms
5905  
Num Waters
536  
Num Hetatoms
278  
Model mean isotropic B factor
28.910Å2  
RMSD bond length
0.007Å  
RMSD bond angle
1.228°  
RMSD dihedral angle
16.111°
 
Filename uploaded
dep.pdb (uploaded on Feb 24, 2011 6:15 PM)  
Inserted
Feb 24, 2011