5XNF

Crystal structure of the branched-chain polyamine synthase (BpsA) from Thermococcus kodakarensis

5XNF の概要

• エントリーDOI: 10.2210/pdb5xnf/pdb
• 分子名称: N(4)-bis(aminopropyl)spermidine synthase, FE (III) ION, SULFATE ION, ... (5 entities in total)
• 機能のキーワード: transferase, polyamine biosynthesis, n(4)-bis(aminopropyl)spermidine synthase
• 由来する生物種: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 85231.95

構造登録者

Mizohata, E.,Tse, K.M.,Fujita, J.,Inoue, T. (登録日: 2017-05-22, 公開日: 2018-08-15, 最終更新日: 2023-11-22)

主引用文献

Hidese, R.,Tse, K.M.,Kimura, S.,Mizohata, E.,Fujita, J.,Horai, Y.,Umezawa, N.,Higuchi, T.,Niitsu, M.,Oshima, T.,Imanaka, T.,Inoue, T.,Fujiwara, S.
Active site geometry of a novel aminopropyltransferase for biosynthesis of hyperthermophile-specific branched-chain polyamine.
FEBS J., 284:3684-3701, 2017

PubMed Abstract: Branched-chain polyamines are found exclusively in thermophilic bacteria and Euryarchaeota and play essential roles in survival at high temperatures. In the present study, kinetic analyses of a branched-chain polyamine synthase from the hyperthermophilic archaeon Thermococcus kodakarensis (Tk-BpsA) were conducted, showing that N -bis(aminopropyl)spermidine was produced by sequential additions of decarboxylated S-adenosylmethionine (dcSAM) aminopropyl groups to spermidine, through bifunctional catalytic action. Tk-BpsA catalyzed the aminopropylation of the linear-chain polyamines spermidine, spermine, norspermidine, and the tertiary-branched polyamines N -aminopropylspermidine and N -aminopropylnorspermidine, but not of short-chain diamines, putrescine, and cadaverine, suggesting that Tk-BpsA does not catalyze the aminopropylation of primary amino groups of diamines. X-ray structural analyses of Tk-BpsA in the presence or absence of the substrates spermidine and dcSAM revealed that a large, negatively charged cavity is responsible for the binding of branched-chain substrates. The binding is different from that in the active site of linear polyamine spermidine/spermine synthases, and loop-closures occur upon the binding of spermidine. Based on structural analyses, further kinetic studies were carried out for various mutants, revealing that Asp159, positioned between the reactive secondary amino group of the substrate polyamine and a sulfur atom of the product 5'-methylthioadenosine and in a Gly-Asp-Asp-Asp motif, functions as a catalytic center, with reactions proceeding via a ping-pong mechanism. Our study provides a novel aminopropyltransfer reaction mechanism, distinct from the S 2 displacement mechanism found in other known linear spermidine/spermine synthases.

PubMed: 28881427
DOI: 10.1111/febs.14262

実験手法

X-RAY DIFFRACTION (1.9 Å)