› 5hr6

X-ray diffraction
2.88Å resolution

X-ray crystal structure of C118A RlmN with cross-linked tRNA purified from Escherichia coli

Released:
DOI: 10.2210/pdb5hr6/pdb
PDB entry 5hr6 coloured by chain, front view.
PDB entry 5hr6 coloured by chain, side view.
PDB entry 5hr6 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Crystallographic capture of a radical S-adenosylmethionine enzyme in the act of modifying tRNA.
Schwalm EL, Grove TL, Booker SJ, Boal AK
Science 352 309-12 (2016)
PMID: 27081063

Function and Biology Details

Reaction catalysed: 
2 S-adenosyl-L-methionine + adenine(2503) in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine(2503) in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153277 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Dual-specificity RNA methyltransferase RlmN Chains: A, B
Molecule details ›
Chains: A, B
Length: 404 amino acids
Theoretical weight: 45.3 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P36979 (Residues: 1-384; Coverage: 100%)
Gene names: JW2501, b2517, rlmN, yfgB
Sequence domains:
Structure domains:
tRNA Glu Chains: C, D
Molecule details ›
Chains: C, D
Length: 68 nucleotides
Theoretical weight: 21.81 KDa
Source organism: Escherichia coli
Sequence domains: tRNA

Ligands and Environments

4 bound ligands:
Ligand MET 2 x MET
Ligand SF4 2 x SF4
Ligand 5AD 2 x 5AD
Ligand MG 6 x MG
1 modified residue:
Ligand SMC 2 x SMC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P21
Unit cell:
a: 88.664Å b: 69.821Å c: 149.298Å
α: 90° β: 90.3° γ: 90°
R-values:
R R work R free
0.184 0.182 0.228
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Naturally occurring modified ribonucleosides.
McCown et al. (2020)
4 more

5 mentions without citation

The diverse structural modes of tRNA binding and recognition.
Biela et al. (2023)
4 more