PDBsum entry 2z3h

Hydrolase

PDB id: 2z3h

Contents

Protein chains

122 a.a. *

Ligands

BLO ×4

Metals

_ZN ×4

Waters ×686

* Residue conservation analysis

PDB id:

2z3h

Name:

Hydrolase

Title:

Crystal structure of blasticidin s deaminase (bsd) complexed with deaminohydroxy blasticidin s

Structure:

Blasticidin-s deaminase. Chain: a, b, c, d. Engineered: yes

Source:

Aspergillus terreus. Organism_taxid: 33178. Strain: s-712. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.50Å R-factor: 0.173 R-free: 0.185

Authors:

T.Kumasaka,M.Yamamoto,M.Furuichi,M.Nakasako,M.Kimura,I.Yamaguchi, T.Ueki

Key ref:

T.Kumasaka et al. (2007). Crystal Structures of Blasticidin S Deaminase (BSD): IMPLICATIONS FOR DYNAMIC PROPERTIES OF CATALYTIC ZINC. J Biol Chem, 282, 37103-37111. PubMed id: 17959604 DOI: 10.1074/jbc.M704476200

Date:

04-Jun-07 Release date: 23-Oct-07

Protein chains

P0C2P0  (BSD_ASPTE) -  Blasticidin-S deaminase from Aspergillus terreus

Seq: 130 a.a.

Struc: 122 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.4.23 - blasticidin-S deaminase.
• Reaction: blasticidin S + H2O + H⁺ = deaminohydroxyblasticidin S + NH4⁺

blasticidin S + H2O + H(+) = deaminohydroxyblasticidin S (Bound ligand (Het Group name = BLO) corresponds exactly) + NH4(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M704476200

J Biol Chem 282:37103-37111 (2007)

PubMed id: 17959604

Crystal Structures of Blasticidin S Deaminase (BSD): IMPLICATIONS FOR DYNAMIC PROPERTIES OF CATALYTIC ZINC.

T.Kumasaka, M.Yamamoto, M.Furuichi, M.Nakasako, A.H.Teh, M.Kimura, I.Yamaguchi, T.Ueki.

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.

Selected figure(s)

Figure 3.
Structural comparison of catalytic center and tetrameric interface.A, BSD; B, BSD R90K mutant; C, EcCDA; D, BsCDA; E, MmCDA. D and E show that 16 and 18 water molecules occupied the region, respectively. The central cavities are drawn as gray surfaces. There is no cavity in BSD or its mutant.

Figure 4.
Tetrahedral and trigonal bipyramidal coordinations of zinc with omit F[O] - F[C] maps.A, native; B, B-subunit of substrate complex. Number sign (#) indicates Ser^86 carbonyl oxygen. C, A-subunit of substrate complex. All the omit F[O] - F[C] maps contoured at the 4.0σ level. Five omitted groups are shown in different colors: zinc (yellow); Cys^54, Cys^88, and Cys^91 (orange); Glu^56 (magenta); Arg^90 (lime); fourth and fifth ligands (cyan). Only in the calculation of fourth and fifth ligands were an additional twenty refinement cycles by Refmac performed to eliminate model bias.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 37103-37111) copyright 2007.

Figures were selected by an automated process.