PDBsum entry 1qaq

Transferase

PDB id: 1qaq

Contents

Protein chain

236 a.a. *

Ligands

SFG

* Residue conservation analysis

PDB id:

1qaq

Name:

Transferase

Title:

The structure of the rrna methyltransferase ermc': implications for the reaction mechanism

Structure:

Ermc' rrna methyltransferase. Chain: a. Synonym: rrna adenine n-6-methyltransferase. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.80Å R-factor: 0.229 R-free: 0.284

Authors:

G.Schluckebier,P.Zhong,K.D.Stewart,T.J.Kavanaugh,C.Abad-Zapatero

Key ref:

G.Schluckebier et al. (1999). The 2.2 A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism. J Mol Biol, 289, 277-291. PubMed id: 10366505 DOI: 10.1006/jmbi.1999.2788

Date:

28-Mar-99 Release date: 29-Mar-00

Protein chain

P13956  (ERM_BACIU) -  rRNA adenine N-6-methyltransferase from Bacillus subtilis

Seq: 244 a.a.

Struc: 236 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.184 - 23S rRNA (adenine(2085)-N(6))-dimethyltransferase.
• Reaction: adenosine₂₀₈₅ in 23S rRNA + 2 S-adenosyl-L-methionine = N₆- dimethyladenosine₂₀₈₅ in 23S rRNA + 2 S-adenosyl-L-homocysteine + 2 H⁺

adenosine(2085) in 23S rRNA + 2 × S-adenosyl-L-methionine = N(6)- dimethyladenosine(2085) in 23S rRNA + 2 × S-adenosyl-L-homocysteine + 2 × H(+) (Bound ligand (Het Group name = SFG) matches with 51.43% similarity)

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

Added reference

DOI no: 10.1006/jmbi.1999.2788

J Mol Biol 289:277-291 (1999)

PubMed id: 10366505

The 2.2 A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism.

G.Schluckebier, P.Zhong, K.D.Stewart, T.J.Kavanaugh, C.Abad-Zapatero.

ABSTRACT

The rRNA methyltransferase ErmC' transfers methyl groups from S -adenosyl-l-methionine to atom N6 of an adenine base within the peptidyltransferase loop of 23 S rRNA, thus conferring antibiotic resistance against a number of macrolide antibiotics. The crystal structures of ErmC' and of its complexes with the cofactor S -adenosyl-l-methionine, the reaction product S-adenosyl-l-homocysteine and the methyltransferase inhibitor Sinefungin, respectively, show that the enzyme undergoes small conformational changes upon ligand binding. Overall, the ligand molecules bind to the protein in a similar mode as observed for other methyltransferases. Small differences between the binding of the amino acid parts of the different ligands are correlated with differences in their chemical structure. A model for the transition-state based on the atomic details of the active site is consistent with a one-step methyl-transfer mechanism and might serve as a first step towards the design of potent Erm inhibitors.

Selected figure(s)

Figure 3.

Figure 4.
Figure 4. Comparison of the AdoMet conformation when bound to different AdoMet-dependent MTases: M. TaqI (blue, PDB entry 2ADM; [Schluckebier et al 1998]), catechol-O-MTase (red, 1VID; [Vidgren et al 1994]), RNA-O2′-MTase VP39 (green, 1VPT; [Hodel et al 1996]) and ErmC′ (this work). AdoMet was superimposed at the adenine rings. Prepared with QUANTA.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 289, 277-291) copyright 1999.

Figures were selected by an automated process.