PDBsum entry 7o5h

Ribosome

PDB id: 7o5h

Contents

Protein chains

251 a.a.

225 a.a.

205 a.a.

158 a.a.

103 a.a.

129 a.a.

117 a.a.

123 a.a.

87 a.a.

82 a.a.

79 a.a.

55 a.a.

86 a.a.

30 a.a.

DNA/RNA

Metals

_MG ×167

PDB id:

7o5h

Name:

Ribosome

Title:

Ribosomal methyltransferase ksga bound to small ribosomal subunit

Structure:

Ribosomal RNA small subunit methyltransferase a. Chain: v. Synonym: 16s rrna (adenine(1518)-n(6)/adenine(1519)-n(6))- dimethyltransferase,16s rrna dimethyladenosine transferase,16s rrna dimethylase,s-adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase. Engineered: yes. 16s rrna. Chain: a.

Source:

Escherichia coli (strain k12). Organism_taxid: 83333. Strain: k12. Gene: rsma, ksga, faz83_07175. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Escherichia coli. Organism_taxid: 562. Strain: jw0050.3.

Authors:

N.C.Stephan,A.B.Ries,D.Boehringer,N.Ban

Key ref:

N.C.Stephan et al. (2021). Structural basis of successive adenosine modifications by the conserved ribosomal methyltransferase KsgA. Nucleic Acids Res, 49, 6389-6398. PubMed id: 34086932 DOI: 10.1093/nar/gkab430

Date:

08-Apr-21 Release date: 16-Jun-21

Protein chain

P06992  (RSMA_ECOLI) -  Ribosomal RNA small subunit methyltransferase A from Escherichia coli (strain K12)

Seq: 273 a.a.

Struc: 251 a.a.

Protein chain

P0A7V0  (RS2_ECOLI) -  Small ribosomal subunit protein uS2 from Escherichia coli (strain K12)

Seq: 241 a.a.

Struc: 225 a.a.

Protein chain

P0A7V8  (RS4_ECOLI) -  Small ribosomal subunit protein uS4 from Escherichia coli (strain K12)

Seq: 206 a.a.

Struc: 205 a.a.

Protein chain

P0A7W1  (RS5_ECOLI) -  Small ribosomal subunit protein uS5 from Escherichia coli (strain K12)

Seq: 167 a.a.

Struc: 158 a.a.

Protein chain

P02358  (RS6_ECOLI) -  Small ribosomal subunit protein bS6 from Escherichia coli (strain K12)

Seq: 135 a.a.

Struc: 103 a.a.

Protein chain

P0A7W7  (RS8_ECOLI) -  Small ribosomal subunit protein uS8 from Escherichia coli (strain K12)

Seq: 130 a.a.

Struc: 129 a.a.

Protein chain

P0A7R9  (RS11_ECOLI) -  Small ribosomal subunit protein uS11 from Escherichia coli (strain K12)

Seq: 129 a.a.

Struc: 117 a.a.

Protein chain

P0A7S3  (RS12_ECOLI) -  Small ribosomal subunit protein uS12 from Escherichia coli (strain K12)

Seq: 124 a.a.

Struc: 123 a.a.

Protein chain

P0ADZ4  (RS15_ECOLI) -  Small ribosomal subunit protein uS15 from Escherichia coli (strain K12)

Seq: 89 a.a.

Struc: 87 a.a.

Protein chain

P0A7T3  (RS16_ECOLI) -  Small ribosomal subunit protein bS16 from Escherichia coli (strain K12)

Seq: 82 a.a.

Struc: 82 a.a.

Protein chain

P0AG63  (RS17_ECOLI) -  Small ribosomal subunit protein uS17 from Escherichia coli (strain K12)

Seq: 84 a.a.

Struc: 79 a.a.

Protein chain

P0A7T7  (RS18_ECOLI) -  Small ribosomal subunit protein bS18 from Escherichia coli (strain K12)

Seq: 75 a.a.

Struc: 55 a.a.

Protein chain

P0A7U7  (RS20_ECOLI) -  Small ribosomal subunit protein bS20 from Escherichia coli (strain K12)

Seq: 87 a.a.

Struc: 86 a.a.

Protein chain

P68679  (RS21_ECOLI) -  Small ribosomal subunit protein bS21 from Escherichia coli (strain K12)

Seq: 71 a.a.

Struc: 30 a.a.

DNA/RNA chain

A-A-A-U-U-G-A-A-G-A-G-U-U-U-G-A-U-C-A-U-G-G-C-U-C-A-G-A-U-U-G-A-A-C-G-C-U-G-G- ... 964 bases

Enzyme reactions

• Enzyme class 2: Chains B, D, E, F, H, K, L, O, P, Q, R, T, U: E.C.?
• Enzyme class 3: Chain V: E.C.2.1.1.182 - 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase.
• Reaction: adenosine₁₅₁₈/adenosine₁₅₁₉ in 16S rRNA + 4 S-adenosyl-L-methionine = N₆-dimethyladenosine₁₅₁₈/N₆-dimethyladenosine₁₅₁₉ in 16S rRNA + 4 S-adenosyl-L-homocysteine + 4 H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

DOI no: 10.1093/nar/gkab430

Nucleic Acids Res 49:6389-6398 (2021)

PubMed id: 34086932

Structural basis of successive adenosine modifications by the conserved ribosomal methyltransferase KsgA.

N.C.Stephan, A.B.Ries, D.Boehringer, N.Ban.

ABSTRACT

Biogenesis of ribosomal subunits involves enzymatic modifications of rRNA that fine-tune functionally important regions. The universally conserved prokaryotic dimethyltransferase KsgA sequentially modifies two universally conserved adenosine residues in helix 45 of the small ribosomal subunit rRNA, which is in proximity of the decoding site. Here we present the cryo-EM structure of Escherichia coli KsgA bound to an E. coli 30S at a resolution of 3.1 Å. The high-resolution structure reveals how KsgA recognizes immature rRNA and binds helix 45 in a conformation where one of the substrate nucleotides is flipped-out into the active site. We suggest that successive processing of two adjacent nucleotides involves base-flipping of the rRNA, which allows modification of the second substrate nucleotide without dissociation of the enzyme. Since KsgA is homologous to the essential eukaryotic methyltransferase Dim1 involved in 40S maturation, these results have also implications for understanding eukaryotic ribosome maturation.