Crystal structures of blasticidin S deaminase (BSD): Implications for dynamic properties of catalytic zinc

Takashi Kumasaka, Masaki Yamamoto, Makio Furuichi, Masayoshi Nakasako, Aik Hong Teh, Makoto Kimura, Isamu Yamaguchi, Tatzuo Ueki

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

The set of blasticidin S (BS) and blasticidin S deaminase (BSD) is a widely used selectable marker for gene transfer experiments. BSD is a member of the cytidine deaminase (CDA) family; it is a zinc-dependent enzyme with three cysteines and one water molecule as zinc ligands. The crystal structures of BSD were determined in six states (i.e. native, substrate-bound, product-bound, cacodylate-bound, substrate-bound E56Q mutant, and R90K mutant). In the structures, the zinc position and coordination structures vary. The substrate-bound structure shows a large positional and geometrical shift of zinc with a double-headed electron density of the substrate that seems to be assigned to the amino and hydroxyl groups of the substrate and product, respectively. In this intermediate-like structure, the steric hindrance of the hydroxyl group pushes the zinc into the triangular plane consisting of three cysteines with a positional shift of ∼0.6 Å, and the fifth ligand water approaches the opposite direction of the substrate with a shift of 0.4 Å. Accordingly, the zinc coordination is changed from tetrahedral to trigonal bipyramidal, and its coordination distance is extended between zinc and its intermediate. The shift of zinc and the recruited water is also observed in the structure of the inactivated E56Q mutant. This novel observation is different in two-cysteine cytidine deaminase Escherichia coli CDA and might be essential for the reaction mechanism in BSD, since it is useful for the easy release of the product by charge compensation and for the structural change of the substrate.

Original languageEnglish
Pages (from-to)37103-37111
Number of pages9
JournalJournal of Biological Chemistry
Volume282
Issue number51
DOIs
Publication statusPublished - 2007 Dec 21

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blasticidin S deaminase
Zinc
Crystal structure
Cytidine Deaminase
Substrates
Cysteine
Hydroxyl Radical
Water
Cacodylic Acid
Ligands
Gene transfer

ASJC Scopus subject areas

  • Biochemistry

Cite this

Crystal structures of blasticidin S deaminase (BSD) : Implications for dynamic properties of catalytic zinc. / Kumasaka, Takashi; Yamamoto, Masaki; Furuichi, Makio; Nakasako, Masayoshi; Teh, Aik Hong; Kimura, Makoto; Yamaguchi, Isamu; Ueki, Tatzuo.

In: Journal of Biological Chemistry, Vol. 282, No. 51, 21.12.2007, p. 37103-37111.

Research output: Contribution to journalArticle

Kumasaka, T, Yamamoto, M, Furuichi, M, Nakasako, M, Teh, AH, Kimura, M, Yamaguchi, I & Ueki, T 2007, 'Crystal structures of blasticidin S deaminase (BSD): Implications for dynamic properties of catalytic zinc', Journal of Biological Chemistry, vol. 282, no. 51, pp. 37103-37111. https://doi.org/10.1074/jbc.M704476200
Kumasaka, Takashi ; Yamamoto, Masaki ; Furuichi, Makio ; Nakasako, Masayoshi ; Teh, Aik Hong ; Kimura, Makoto ; Yamaguchi, Isamu ; Ueki, Tatzuo. / Crystal structures of blasticidin S deaminase (BSD) : Implications for dynamic properties of catalytic zinc. In: Journal of Biological Chemistry. 2007 ; Vol. 282, No. 51. pp. 37103-37111.
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