PDBsum entry 5f8c

Transferase

PDB id: 5f8c

Contents

Protein chains

354 a.a.

Ligands

GOL ×4

Waters ×719

PDB id:

5f8c

Name:

Transferase

Title:

Rv2258c-unbound

Structure:

Methyltransferase. Chain: a, b, c. Synonym: possible transcriptional regulatory protein. Engineered: yes

Source:

Mycobacterium tuberculosis h37rv. Organism_taxid: 83332. Strain: h37rv. Gene: rv2258c, lh57_12310. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.83Å R-factor: 0.193 R-free: 0.226

Authors:

H.N.Im,S.W.Suh

Key ref:

H.N.Im et al. (2016). Crystal structure of Rv2258c from Mycobacterium tuberculosis H37Rv, an S-adenosyl-l-methionine-dependent methyltransferase. J Struct Biol, 193, 172-180. PubMed id: 26772148 DOI: 10.1016/j.jsb.2016.01.002

Date:

09-Dec-15 Release date: 29-Jun-16

Protein chains

O53532  (O53532_MYCTU) -  S-adenosylmethionine-dependent methyltransferase Rv2258c from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 353 a.a.

Struc: 354 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.1.1.- - ?????

DOI no: 10.1016/j.jsb.2016.01.002

J Struct Biol 193:172-180 (2016)

PubMed id: 26772148

Crystal structure of Rv2258c from Mycobacterium tuberculosis H37Rv, an S-adenosyl-l-methionine-dependent methyltransferase.

H.N.Im, H.S.Kim, D.R.An, J.Y.Jang, J.Kim, H.J.Yoon, J.K.Yang, S.W.Suh.

ABSTRACT

The Mycobacterium tuberculosis Rv2258c protein is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase (MTase). Here, we have determined its crystal structure in three forms: a ligand-unbound form, a binary complex with sinefungin (SFG), and a binary complex with S-adenosyl-L-homocysteine (SAH). The monomer structure of Rv2258c consists of two domains which are linked by a long α-helix. The N-terminal domain is essential for dimerization and the C-terminal domain has the Class I MTase fold. Rv2258c forms a homodimer in the crystal, with the N-terminal domains facing each other. It also exists as a homodimer in solution. A DALI structural similarity search with Rv2258c reveals that the overall structure of Rv2258c is very similar to small-molecule SAM-dependent MTases. Rv2258c interacts with the bound SFG (or SAH) in an extended conformation maintained by a network of hydrogen bonds and stacking interactions. Rv2258c has a relatively large hydrophobic cavity for binding of the methyl-accepting substrate, suggesting that bulky nonpolar molecules with aromatic rings might be targeted for methylation by Rv2258c in M. tuberculosis. However, the ligand-binding specificity and the biological role of Rv2258c remain to be elucidated due to high variability of the amino acid residues defining the substrate-binding site.