PDBsum entry 4l69

Transferase

PDB id

4l69

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Contents

			Protein chain

					244 a.a.

			Waters ×19

PDB id:

4l69

Links

Name:

Transferase

Title:

Rv2372c of mycobacterium tuberculosis is rsme like methyltransferse

Structure:

Ribosomal RNA small subunit methyltransferase e. Chain: a. Synonym: 16s rrna m3u1498 methyltransferase. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Strain: h37rv. Gene: mt2441, mtcy27.08, rsme, rv2372c. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.90Å

R-factor:

0.201

R-free:

0.236

Authors:

A.Kumar,B.Taneja

Key ref:

A.Kumar et al. (2014). The structure of Rv2372c identifies an RsmE-like methyltransferase from Mycobacterium tuberculosis. Acta Crystallogr D Biol Crystallogr, 70, 821-832. PubMed id: 24598751 DOI: 10.1107/S1399004713033555

Date:

12-Jun-13

Release date:

19-Mar-14

PROCHECK

	Headers

	References

Protein chain

P9WGX1 (RSME_MYCTU) - Ribosomal RNA small subunit methyltransferase E from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: Struc:					262 a.a. 244 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.2.1.1.193 - 16S rRNA (uracil(1498)-N(3))-methyltransferase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

uridine₁₄₉₈ in 16S rRNA + S-adenosyl-L-methionine = N₃- methyluridine₁₄₉₈ in 16S rRNA + S-adenosyl-L-homocysteine + H⁺

uridine(1498) in 16S rRNA	+	S-adenosyl-L-methionine	=	N(3)- methyluridine(1498) in 16S rRNA	+	S-adenosyl-L-homocysteine	+	H(+)

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

Added reference

DOI no: 10.1107/S1399004713033555	Acta Crystallogr D Biol Crystallogr 70:821-832 (2014)
PubMed id: 24598751

The structure of Rv2372c identifies an RsmE-like methyltransferase from Mycobacterium tuberculosis.
A.Kumar, S.Kumar, B.Taneja.

ABSTRACT

U1498 of 16S rRNA plays an important role in translation fidelity as well as in antibiotic response. U1498 is present in a methylated form in the decoding centre of the ribosome. In this study, Rv2372c from Mycobacterium tuberculosis has been identified as an RsmE-like methyltransferase which specifically methylates U1498 of 16S rRNA at the N3 position and can complement RsmE-deleted Escherichia coli. The crystal structure of Rv2372c has been determined, and reveals that the protein belongs to a distinct class in the SPOUT superfamily and exists as a dimer. The deletion of critical residues at the C-terminus of Rv2372c leads to an inability of the protein to form stable dimers and to abolition of the methyltransferase activity. A ternary model of Rv2372c with its cofactor S-adenosylmethionine (SAM) and the 16S rRNA fragment (1487)16S rRNA(1510) helps to identify binding pockets for SAM (in the deep trefoil knot) and substrate RNA (at the dimer interface) and suggests an SN2 mechanism for the methylation of N3 of U1498 in 16S rRNA.