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X-ray structure of RlmN from Escherichia coli

Source organism: Escherichia coli K-12
Biochemical function: rRNA (adenine(2503)-C2-)-methyltransferase activity
Biological process: rRNA base methylation
Cellular component: cytosol

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EC 2.1.1.192: 23S rRNA (adenine(2503)-C(2))-methyltransferase

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
Systematic name:
S-adenosyl-L-methionine:23S rRNA (adenine(2503)-C(2))-methyltransferase
Alternative Name(s):
  • Cfr
  • RlmN
  • YfgB

GO terms

Sequence families

Pfam Protein families (Pfam)
PF04055
Domain description: Radical SAM superfamily
Occurring in:
  1. Dual-specificity RNA methyltransferase RlmN
The deposited structure of PDB entry 3rf9 contains 2 copies of Pfam domain PF04055 (Radical SAM superfamily) in Dual-specificity RNA methyltransferase RlmN. Showing 1 copy in chain A.

PF21016
Domain description: Ribosomal RNA large subunit methyltransferase N-terminal domain
Occurring in:
  1. Dual-specificity RNA methyltransferase RlmN
The deposited structure of PDB entry 3rf9 contains 2 copies of Pfam domain PF21016 (Ribosomal RNA large subunit methyltransferase N-terminal domain) in Dual-specificity RNA methyltransferase RlmN. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR007197
Domain description: Radical SAM
Occurring in:
  1. Dual-specificity RNA methyltransferase RlmN
IPR027492
Domain description: Dual-specificity RNA methyltransferase RlmN
Occurring in:
  1. Dual-specificity RNA methyltransferase RlmN
IPR004383
Domain description: Ribosomal RNA large subunit methyltransferase RlmN/Cfr
Occurring in:
  1. Dual-specificity RNA methyltransferase RlmN
IPR013785
Domain description: Aldolase-type TIM barrel
Occurring in:
  1. Dual-specificity RNA methyltransferase RlmN
IPR040072
Domain description: Methyltransferase (Class A)
Occurring in:
  1. Dual-specificity RNA methyltransferase RlmN

Structure domains

CATH CATH domains
3.20.20.70
Class: Alpha Beta
Architecture: Alpha-Beta Barrel
Topology: TIM Barrel
Homology: Aldolase class I
Occurring in:
  1. Dual-specificity RNA methyltransferase RlmN
The deposited structure of PDB entry 3rf9 contains 2 copies of CATH domain 3.20.20.70 (TIM Barrel) in Dual-specificity RNA methyltransferase RlmN. Showing 1 copy in chain A.
1.10.150.530
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: DNA polymerase; domain 1
Homology: DNA polymerase; domain 1
Occurring in:
  1. Dual-specificity RNA methyltransferase RlmN
The deposited structure of PDB entry 3rf9 contains 2 copies of CATH domain 1.10.150.530 (DNA polymerase; domain 1) in Dual-specificity RNA methyltransferase RlmN. Showing 1 copy in chain A.
4.10.180.60
Class: Few Secondary Structures
Architecture: Irregular
Topology: Black beetle virus capsid protein
Homology: Black beetle virus capsid protein
Occurring in:
  1. Dual-specificity RNA methyltransferase RlmN
The deposited structure of PDB entry 3rf9 contains 1 copy of CATH domain 4.10.180.60 (Black beetle virus capsid protein) in Dual-specificity RNA methyltransferase RlmN. Showing 1 copy in chain A.

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