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'''Crystal Structure of Blasticidin S Deaminase (BSD) Complexed with Tetrahedral Intermediate of Blasticidin S''' | '''Crystal Structure of Blasticidin S Deaminase (BSD) Complexed with Tetrahedral Intermediate of Blasticidin S''' | ||
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==Overview== | ==Overview== | ||
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 approximately 0.6 A, and the fifth ligand water approaches the opposite direction of the substrate with a shift of 0.4 A. 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. | |||
==About this Structure== | ==About this Structure== | ||
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==Reference== | ==Reference== | ||
Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc., Kumasaka T, Yamamoto M, Furuichi M, Nakasako M, Teh AH, Kimura M, Yamaguchi I, Ueki T, J Biol Chem. 2007 Dec 21;282(51):37103-11. Epub 2007 Oct 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17959604 17959604] | |||
[[Category: Aspergillus terreus]] | [[Category: Aspergillus terreus]] | ||
[[Category: Blasticidin-S deaminase]] | [[Category: Blasticidin-S deaminase]] | ||
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[[Category: Yamaguchi, I.]] | [[Category: Yamaguchi, I.]] | ||
[[Category: Yamamoto, M.]] | [[Category: Yamamoto, M.]] | ||
[[Category: | [[Category: Cytidine deaminase family]] | ||
[[Category: | [[Category: Hydrolase]] | ||
[[Category: | [[Category: Tetramer]] | ||
[[Category: | [[Category: Zinc]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 30 13:22:25 2008'' | |||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | |||
Revision as of 13:22, 30 April 2008
Crystal Structure of Blasticidin S Deaminase (BSD) Complexed with Tetrahedral Intermediate of Blasticidin S
OverviewOverview
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 approximately 0.6 A, and the fifth ligand water approaches the opposite direction of the substrate with a shift of 0.4 A. 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.
About this StructureAbout this Structure
1WN6 is a Single protein structure of sequence from Aspergillus terreus. Full crystallographic information is available from OCA.
ReferenceReference
Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc., Kumasaka T, Yamamoto M, Furuichi M, Nakasako M, Teh AH, Kimura M, Yamaguchi I, Ueki T, J Biol Chem. 2007 Dec 21;282(51):37103-11. Epub 2007 Oct 23. PMID:17959604 Page seeded by OCA on Wed Apr 30 13:22:25 2008