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Structure of IDP01693

STRUCTURE OF IDP01693/YJEA, POTENTIAL T-RNA SYNTHETASE FROM SALMONELLA TYPHIMURIUM

Edit deposit information
CSGID target
IDP01693 
PDB Id
3G1Z (NCBI MMDB
Authors
A.U.Singer,E.Evdokimova,M.Kudritska,M.E.Cuff,A.M.Edwards,W.F.Anderson,A.Savchenko,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Alexander Singer 
Responsible lab
University of Calgary 
Deposition Date
Jan 30, 2009 
Release Date
Mar 10, 2009 

Annotation

Description
Note – our collaborators also call it PoxA Description: This is an usual lysyl tRNA synthetase, also named Lysine-tRNA ligase, which belongs to the class II aminoacyl-tRNA synthetases. The structure shows an anti-parallel beta-sheet fold flanked by alpha-helices and was found as a dimer, however it lacks an tRNA anticodon-binding domain. For example, comparing it to the E. coli lysyl tRNA synthetase (LysU) residues 5-325 of PoxA overlay with residues 167-502 of LysU (in complex with AMPCP and lysine, PDB code 1E22) with an RMSD of 1.9 A, a Z-score of 11.4 and 45 residues are identical in this alignment. A similar structure apparently has been solved in Pyrococcus furiosis (PDB code 1NNH); this structure also is a smaller version of a tRNA synthetase (294 residues) with a catalytic domain and no anticodon-binding domain; this protein overlays with the PoxA structure with a Z-score of 10.1 and an RMSD of 1.9 A. Crystals of the apo-structure were hard to achieve; however the protein crystallized readily in the presence of ATP. Our first structure contains a single bound AMP for each PoxA molecule; from the structure residues binding the nucleotide include F112 and R303, whose side chains stack on either side of the adenine ring, E102 whose carboxyl group hydrogen-bonds to the N2 NH of the adenine ring, and R100, whose guanidium group forms a salt bridge with the alpha phosphate of the AMP. In overlaying the structure of 1E22 (LysU plus AMPCP) with the PoxA/AMP structure, one observes an additional phosphate group in the PoxA structure occupying a position midway between the beta and gamma phosphates of the AMPCP molecule in the LysU structure. This phosphate is hydrogen-bonded by the side chains of H108 and E244. At present we are working on solving the structure of PoxA with a non-hydrolyzable ATP analogue. Our collaborator William Navarre at University of Toronto has been involved in determination of its amino acid substrate and its role in Salmonella pathogenesis, and this combination of structural, biochemical and microbiological work will form the basis of a manuscript in the not to near future. 
Functional assignment
tRNA synthetase 

Ligands

Ligand code Name Ligand type
AMP biological
CL
PO4 PHOSPHATE ION

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=69.90Å, b=68.91Å, c=73.27Å
α=90.00, β=110.31, γ=90.00 
Solvent content
45.06  
Matthews coefficient
2.24  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
47.51-1.95Å (2.00-1.95Å)  
Rall(%)
18.4 
Rwork(%)
18.1 (21.2) 
Rfree(%)
23.9 (30.2) 
Num. observed reflections
46299 (3509) 
Num. Rfree reflections
2361 (191) 
Completeness(%)
97.0 (100.0) 

Model parameters

Num Atoms
5950  
Num Waters
645  
Num Hetatoms
0  
Model mean isotropic B factor
25.664Å2  
RMSD bond length
0.013Å  
RMSD bond angle
1.436°  
Filename uploaded
new_start_cut1_refmac22b.pdb (uploaded on Feb 04, 2009 6:33 PM)  
Inserted
Feb 04, 2009