› 4blw

X-ray diffraction
1.95Å resolution

Crystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyltransferase RlmJ in complex with S-adenosylhomocysteine (AdoHcy) and Adenosine monophosphate (AMP)

Released:
DOI: 10.2210/pdb4blw/pdb
PDB entry 4blw coloured by chain, front view.
PDB entry 4blw coloured by chain, side view.
PDB entry 4blw coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural and functional insights into the molecular mechanism of rRNA m6A methyltransferase RlmJ.
Punekar AS, Liljeruhm J, Shepherd TR, Forster AC, Selmer M
Nucleic Acids Res 41 9537-48 (2013)
PMID: 23945937

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + adenine(2030) in 23S rRNA = S-adenosyl-L-homocysteine + N(6)-methyladenine(2030) in 23S rRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153451 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribosomal RNA large subunit methyltransferase J Chains: A, B
Molecule details ›
Chains: A, B
Length: 289 amino acids
Theoretical weight: 33.09 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P37634 (Residues: 1-280; Coverage: 100%)
Gene names: JW3466, b3499, rlmJ, yhiR
Sequence domains: Ribosomal RNA large subunit methyltransferase D, RlmJ
Structure domains: Vaccinia Virus protein VP39

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
5 bound ligands:
Ligand AMP 2 x AMP
Ligand GOL 3 x GOL
Ligand EDO 14 x EDO
Ligand NA 2 x NA
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Spacegroup: P21
Unit cell:
a: 46.59Å b: 77.06Å c: 84.37Å
α: 90° β: 99.5° γ: 90°
R-values:
R R work R free
0.169 0.167 0.199
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Programming Structured DNA Assemblies to Probe Biophysical Processes.
Wamhoff et al. (2019)
1 more

3 mentions without citation

A comprehensive review of m6A/m6Am RNA methyltransferase structures.
Oerum et al. (2021)
2 more