Structure of IDP04643
Crystal Structure of Phosphoribosylaminoimidazole Synthetase from Francisella tularensis
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
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Ligands
| Ligand code | Name | Ligand type |
|---|---|---|
| SO4 | sulfate ion | |
| AMP | adenosine monophosphate | |
| ACY | acetic acid | |
| FMT | formic acid | |
| TRS | 2-amino-2-hydroxymethyl-propane-1,3-diol | |
| MSE | selenomethionine | 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
- Resolution range
- 28.75-1.70Å (1.76-1.70Å)
- Rall(%)
- 15.5
- Rwork(%)/dt>
- 15.4 (17.2)
- Rfree(%)
- 18.3 (21.5)
- Num. observed reflections
- 76345 (5778)
- Num. Rfree reflections
- 3855 (301)
- Completeness(%)
- 96.5 (78.0)
- Num Atoms
- 6757
- Num Waters
- 816
- Num Hetatoms
- 0
- Model mean isotropic B factor (Å2)
- 22.960
- RMSD bond length (Å)
- 0.009
- 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
