PDBsum entry: 2fpo

Transferase

PDB id: 2fpo

Contents

Protein chains

177 a.a. *

177 a.a. *

Ligands

EDO

Metals

_CL ×6

Waters ×390

* Residue conservation analysis

PDB id:

2fpo

Name:

Transferase

Title:

Putative methyltransferase yhhf from escherichia coli.

Structure:

Methylase yhhf. Chain: a, b, c, d, e, f. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: yhhf. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.05Å R-factor: 0.184 R-free: 0.217

Authors:

J.Osipiuk,Y.Kim,R.Sanishvili,T.Skarina,E.Evdokimova,A.Savche A.Edwards,A.Joachimiak,Midwest Center For Structural Genomi

Key ref:

D.V.Lesnyak et al. (2007). Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure. J Biol Chem, 282, 5880-5887. PubMed id: 17189261 DOI: 10.1074/jbc.M608214200

Date:

16-Jan-06 Release date: 28-Feb-06

Protein chains

P0ADX9  (RSMD_ECOLI) -  Ribosomal RNA small subunit methyltransferase D

Seq: 198 a.a.

Struc: 177 a.a.

Protein chain

P0ADX9  (RSMD_ECOLI) -  Ribosomal RNA small subunit methyltransferase D

Seq: 198 a.a.

Struc: 177 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F: E.C.2.1.1.171 - 16S rRNA (guanine(966)-N(2))-methyltransferase.
• Reaction: S-adenosyl-L-methionine + guanosine₉₆₆ in 16S rRNA = S-adenosyl-L- homocysteine + N₂-methylguanosine₉₆₆ in 16S rRNA

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: methylation (4 terms)
• Biochemical function: nucleic acid binding (5 terms)

Added reference

DOI no: 10.1074/jbc.M608214200

J Biol Chem 282:5880-5887 (2007)

PubMed id: 17189261

Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure.

D.V.Lesnyak, J.Osipiuk, T.Skarina, P.V.Sergiev, A.A.Bogdanov, A.Edwards, A.Savchenko, A.Joachimiak, O.A.Dontsova.

ABSTRACT

N(2)-Methylguanine 966 is located in the loop of Escherichia coli 16 S rRNA helix 31, forming a part of the P-site tRNA-binding pocket. We found yhhF to be a gene encoding for m(2)G966 specific 16 S rRNA methyltransferase. Disruption of the yhhF gene by kanamycin resistance marker leads to a loss of modification at G966. The modification could be rescued by expression of recombinant protein from the plasmid carrying the yhhF gene. Moreover, purified m(2)G966 methyltransferase, in the presence of S-adenosylomethionine (AdoMet), is able to methylate 30 S ribosomal subunits that were purified from yhhF knock-out strain in vitro. The methylation is specific for G966 base of the 16 S rRNA. The m(2)G966 methyltransferase was crystallized, and its structure has been determined and refined to 2.05A(.) The structure closely resembles RsmC rRNA methyltransferase, specific for m(2)G1207 of the 16 S rRNA. Structural comparisons and analysis of the enzyme active site suggest modes for binding AdoMet and rRNA to m(2)G966 methyltransferase. Based on the experimental data and current nomenclature the protein expressed from the yhhF gene was renamed to RsmD. A model for interaction of RsmD with ribosome has been proposed.

Selected figure(s)

Figure 4.
FIGURE 4. Structure of the RsmD protein. A, the RsmD protein monomer structure shown as a schematic in rainbow colors with N terminus and C terminus marked in blue and red, respectively (only chain A of the PDB code 2FPO deposit is shown). B, stereo view of representative electron density map showing the RsmD active-site region.

Figure 5.
FIGURE 5. Structure alignment of RsmD protein (shown in "blue") to related rRNA methyltransferases RsmC (shown in orange) (A) and RsmB (shown in magenta) (B).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 5880-5887) copyright 2007.

Figures were selected by an automated process.