Structure of IDP90258

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

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
OCS	cysteinesulfonic acid	crystallization

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

 

Matthews coefficient

 

Refinement

Data for the highest resolution shell is in parentheses.

Resolution range

27.32-2.35Å (2.41-2.35Å)  

R_all(%)

21.1  

R_work(%)

20.9 (26.3)  

R_free(%)

25.5 (32.3)  

Num. observed reflections

14517 (1055)  

Num. R_free reflections

725 (57)  

Completeness(%)

99.8 (100.0)  

Model parameters

Num Atoms

1945  

Num Waters

83  

Num Hetatoms

9  

Model mean isotropic B factor

24.520Ų  

RMSD bond length

0.014Å  

RMSD bond angle

1.746°  

Filename uploaded

rcsb056595.pdb (uploaded on 2009-12-09 18:31:07-05)