2Z3G

Crystal structure of blasticidin S deaminase (BSD)

Summary for 2Z3G

• Entry DOI: 10.2210/pdb2z3g/pdb
• Related: 2Z3H 2Z3I 2Z3J
• Related PRD ID: PRD_900006
• Descriptor: Blasticidin-S deaminase, alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose, ZINC ION, ... (4 entities in total)
• Functional Keywords: hydrolase, cytidine deaminase family, zinc, tetramer
• Biological source: Aspergillus terreus
• Total number of polymer chains: 4
• Total formula weight: 54516.91

Authors

Kumasaka, T.,Yamamoto, M.,Furuichi, M.,Nakasako, M.,Kimura, M.,Yamaguchi, I.,Ueki, T. (deposition date: 2007-06-04, release date: 2007-10-23, Last modification date: 2023-11-01)

Primary citation

Kumasaka, T.,Yamamoto, M.,Furuichi, M.,Nakasako, M.,Teh, A.H.,Kimura, M.,Yamaguchi, I.,Ueki, T.
Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282:37103-37111, 2007

PubMed 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 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.

PubMed: 17959604
DOI: 10.1074/jbc.M704476200

Experimental method

X-RAY DIFFRACTION (1.5 Å)