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Structure of IDP90258

2.35 Angstrom resolution crystal structure of a putative tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus subsp. aureus MRSA252

Edit deposit information
CSGID target
IDP90258 
PDB Id
3KY7 (NCBI MMDB
Authors
A.S.Halavaty,G.Minasov,J.Winsor,I.Dubrovska,L.Shuvalova,R.See,R.Zoraghi,N.Reiner,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Dec 04, 2009 
Release Date
Dec 22, 2009 

Annotation

Description
Methyltransferases (methylases) use S-adenosylmethione (SAM) as a cofactor for tRNA methylation reactions. All five known classes of methyltransferases of the TrmD and SpoU families have a distinct alpha/beta topology and considered to be structurally different enzymes. In the structure of a putative tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus (Staph), two domains, N-terminal SAM-binding domain and C-terminal RNA-binding domain, of the protein are interconnected with a long partially unfolded loop region. The core of the N-terminal domain made up of six parallel beta-strands resembling structural fold of the class IV methylases of the SpoU family. Six strands are flanked by helices with the final three strands are folded into a rare deep trefoil knot, which provides the binding site for the cofactor. TrmD is believed to function as a dimer that is formed in parallel fashion by symmetry operation in the P4332 space group of the Staph protein. Such quaternary architecture localized two active sites in a close proximity to each other. The disordered inter-domain linker is a characteristic feature of the apo-methyltransferases. Based on literature data, the flexible loop between two domains appears to possibly cover the SAM-active site upon binding of the cognate tRNA and providing a candidate for the catalytic base. The C-terminal domain has a lower average B-factor than the catalytic domain and shows structural similarity to DNA-binding domains of trp and tet repressors. Co-crystallization of the Staph TrmD with its cofactor can help in understanding the mechanism and inhibition of the methylation reaction.  
Functional assignment
Methyltransferase 

Ligands

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

Structure information

Unit cell parameters

Space Group
P 43 3 2  
Unit Cell

a=125.18Å, b=125.18Å, c=125.18Å
α=90.00, β=90.00, γ=90.00 
Solvent content
53.56  
Matthews coefficient
2.65  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
27.32-2.35Å (2.41-2.35Å)  
Rall(%)
21.1 
Rwork(%)
20.9 (26.3) 
Rfree(%)
25.5 (32.3) 
Num. observed reflections
14517 (1055) 
Num. Rfree reflections
725 (57) 
Completeness(%)
99.8 (100.0) 

Model parameters

Num Atoms
1850  
Num Waters
83  
Num Hetatoms
95  
Model mean isotropic B factor
24.520Å2  
RMSD bond length
0.014Å  
RMSD bond angle
1.746°  
Filename uploaded
3KY7.pdb (uploaded on Sep 17, 2010 5:37 PM)  
Inserted
Dec 09, 2009