4BLV

Crystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyltransferase RlmJ in complex with S-adenosylmethionine (AdoMet)

Summary for 4BLV

• Entry DOI: 10.2210/pdb4blv/pdb
• Related: 4BLU 4BLW
• Descriptor: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J, S-ADENOSYLMETHIONINE, GLYCEROL, ... (7 entities in total)
• Functional Keywords: transferase, n6-methyladenine, rossmann-like fold, subdomain insertion
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 2
• Total formula weight: 69146.91

Authors

Punekar, A.S.,Liljeruhm, J.,Shepherd, T.R.,Forster, A.C.,Selmer, M. (deposition date: 2013-05-04, release date: 2013-08-21, Last modification date: 2023-12-20)

Primary citation

Punekar, A.S.,Liljeruhm, J.,Shepherd, T.R.,Forster, A.C.,Selmer, M.
Structural and Functional Insights Into the Molecular Mechanism of Rrna M6A Methyltransferase Rlmj.
Nucleic Acids Res., 41:9537-, 2013

PubMed Abstract: RlmJ catalyzes the m(6)A2030 methylation of 23S rRNA during ribosome biogenesis in Escherichia coli. Here, we present crystal structures of RlmJ in apo form, in complex with the cofactor S-adenosyl-methionine and in complex with S-adenosyl-homocysteine plus the substrate analogue adenosine monophosphate (AMP). RlmJ displays a variant of the Rossmann-like methyltransferase (MTase) fold with an inserted helical subdomain. Binding of cofactor and substrate induces a large shift of the N-terminal motif X tail to make it cover the cofactor binding site and trigger active-site changes in motifs IV and VIII. Adenosine monophosphate binds in a partly accommodated state with the target N6 atom 7 Å away from the sulphur of AdoHcy. The active site of RlmJ with motif IV sequence 164DPPY167 is more similar to DNA m(6)A MTases than to RNA m(6)2A MTases, and structural comparison suggests that RlmJ binds its substrate base similarly to DNA MTases T4Dam and M.TaqI. RlmJ methylates in vitro transcribed 23S rRNA, as well as a minimal substrate corresponding to helix 72, demonstrating independence of previous modifications and tertiary interactions in the RNA substrate. RlmJ displays specificity for adenosine, and mutagenesis experiments demonstrate the critical roles of residues Y4, H6, K18 and D164 in methyl transfer.

PubMed: 23945937
DOI: 10.1093/NAR/GKT719

Experimental method

X-RAY DIFFRACTION (2 Å)