5U1I

Crystal structure of a methyltransferase involved in the biosynthesis of gentamicin in complex with the methylated Kanamycin B

5U1I の概要

• エントリーDOI: 10.2210/pdb5u1i/pdb
• 関連するPDBエントリー: 5U0N 5U0T 5U18 5U19 5U1E
• 分子名称: Putative gentamicin methyltransferase, S-ADENOSYL-L-HOMOCYSTEINE, CALCIUM ION, ... (5 entities in total)
• 機能のキーワード: gentamicin methyltransferase sah methylated kanamycin b, transferase
• 由来する生物種: Micromonospora echinospora
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 38373.93

構造登録者

Bury, P.,Huang, F.,Leadlay, P.,Dias, M.V.B. (登録日: 2016-11-28, 公開日: 2017-11-01, 最終更新日: 2023-10-04)

主引用文献

Bury, P.D.S.,Huang, F.,Li, S.,Sun, Y.,Leadlay, P.F.,Dias, M.V.B.
Structural Basis of the Selectivity of GenN, an Aminoglycoside N-Methyltransferase Involved in Gentamicin Biosynthesis.
ACS Chem. Biol., 12:2779-2787, 2017

PubMed Abstract: Gentamicins are heavily methylated, clinically valuable pseudotrisaccharide antibiotics produced by Micromonospora echinospora. GenN has been characterized as an S-adenosyl-l-methionine-dependent methyltransferase with low sequence similarity to other enzymes. It is responsible for the 3″-N-methylation of 3″-dehydro-3″-amino-gentamicin A2, an essential modification of ring III in the biosynthetic pathway to the gentamicin C complex. Purified recombinant GenN also efficiently catalyzes 3″-N-methylation of related aminoglycosides kanamycin B and tobramycin, which both contain an additional hydroxymethyl group at the C5″ position in ring III. We have obtained eight cocrystal structures of GenN, at a resolution of 2.2 Å or better, including the binary complex of GenN and S-adenosyl-l-homocysteine (SAH) and the ternary complexes of GenN, SAH, and several aminoglycosides. The GenN structure reveals several features not observed in any other N-methyltransferase that fit it for its role in gentamicin biosynthesis. These include a novel N-terminal domain that might be involved in protein:protein interaction with upstream enzymes of the gentamicin X2 biosynthesis and two long loops that are involved in aminoglycoside substrate recognition. In addition, the analysis of structures of GenN in complex with different ligands, supported by the results of active site mutagenesis, has allowed us to propose a catalytic mechanism and has revealed the structural basis for the surprising ability of native GenN to act on these alternative substrates.

PubMed: 28876898
DOI: 10.1021/acschembio.7b00466

実験手法

X-RAY DIFFRACTION (1.932 Å)