PDBsum entry 4pl2

Transferase

PDB id: 4pl2

Contents

Protein chains

350 a.a.

Ligands

SF4 ×2

Waters ×231

PDB id:

4pl2

Name:

Transferase

Title:

X-ray crystal structure of c118a rlmn from escherichia coli

Structure:

Dual-specificity RNA methyltransferase rlmn. Chain: b, a. Fragment: unp residues 17-375. Synonym: 23s rrna (adenine(2503)-c(2))-methyltransferase,23s rrna m2a2503 methyltransferase,ribosomal RNA large subunit methyltransferase n,tRNA (adenine(37)-c(2))-methyltransferase,tRNA m2a37 methyltransferase. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 536056. Strain: atcc 33849 / dsm 4235 / ncib 12045 / k12 / dh1. Gene: rlmn, ecdh1_1151, ecdh1me8569_2444. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.20Å R-factor: 0.207 R-free: 0.244

Authors:

A.K.Boal,A.C.Rosenzweig

Key ref:

A.Silakov et al. (2014). Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN. J Am Chem Soc, 136, 8221-8228. PubMed id: 24806349 DOI: 10.1021/ja410560p

Date:

16-May-14 Release date: 28-May-14

Protein chains

C9QPQ6  (C9QPQ6_ECOD1) -

Enzyme reactions

• Enzyme class: E.C.2.1.1.192 - 23S rRNA (adenine(2503)-C(2))-methyltransferase.
• Reaction:
  1. adenosine₂₅₀₃ in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine₂₅₀₃ in 23S rRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine
  2. adenosine₃₇ in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine₃₇ in tRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine
• Cofactor: Iron-sulfur

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

reference

DOI no: 10.1021/ja410560p

J Am Chem Soc 136:8221-8228 (2014)

PubMed id: 24806349

Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN.

A.Silakov, T.L.Grove, M.I.Radle, M.R.Bauerle, M.T.Green, A.C.Rosenzweig, A.K.Boal, S.J.Booker.

ABSTRACT

RlmN and Cfr are methyltransferases/methylsynthases that belong to the radical S-adenosylmethionine superfamily of enzymes. RlmN catalyzes C2 methylation of adenosine 2503 (A2503) of 23S rRNA, while Cfr catalyzes C8 methylation of the exact same nucleotide, and will subsequently catalyze C2 methylation if the site is unmethylated. A key feature of the unusual mechanisms of catalysis proposed for these enzymes is the attack of a methylene radical, derived from a methylcysteine residue, onto the carbon center undergoing methylation to generate a paramagnetic protein-nucleic acid cross-linked species. This species has been thoroughly characterized during Cfr-dependent C8 methylation, but does not accumulate to detectible levels in RlmN-dependent C2 methylation. Herein, we show that inactive C118S/A variants of RlmN accumulate a substrate-derived paramagnetic species. Characterization of this species by electron paramagnetic resonance spectroscopy in concert with strategic isotopic labeling shows that the radical is delocalized throughout the adenine ring of A2503, although predominant spin density is on N1 and N3. Moreover, (13)C hyperfine interactions between the radical and the methylene carbon of the formerly [methyl-(13)C]Cys355 residue show that the radical species exists in a covalent cross-link between the protein and the nucleic acid substrate. X-ray structures of RlmN C118A show that, in the presence of SAM, the substitution does not alter the active site structure compared to that of the wild-type enzyme. Together, these findings have new mechanistic implications for the role(s) of C118 and its counterpart in Cfr (C105) in catalysis, and suggest involvement of the residue in resolution of the cross-linked species via a radical mediated process.