2Z3H

Crystal structure of blasticidin S deaminase (BSD) complexed with deaminohydroxy blasticidin S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

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

(2007) J.Biol.Chem. 282: 37103-37111

  • DOI: 10.1074/jbc.M704476200
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Studies of Blasticidin S Deaminase from Aspergillus Terreus
      Nakasako, M.,Kimura, M.,Yamaguchi, I.
      (1999) Acta Crystallogr.,Sect.D 55: 547


    Organizational Affiliation

    Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan. kumasaka@spring8.or.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Blasticidin-S deaminase
A, B, C, D
130Aspergillus terreusMutation(s): 0 
Gene Names: bsd
EC: 3.5.4.23
Find proteins for P0C2P0 (Aspergillus terreus)
Go to UniProtKB:  P0C2P0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BLO
Query on BLO

Download SDF File 
Download CCD File 
A, B, C, D
1-(4-{[(3R)-3-AMINO-5-{[(Z)-AMINO(IMINO)METHYL](METHYL)AMINO}PENTANOYL]AMINO}-2,3,4-TRIDEOXY-D-ERYTHRO-HEX-2-ENOPYRANURONOSYL)-4-HYDROXYPYRIMIDIN-2(1H)-ONE
DEAMINOHYDROXY BLASTICIDIN-S
C17 H25 N7 O6
REIIQZAQCCFGIJ-ZNIXKSQXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BLOKi: 23000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.300α = 90.00
b = 69.275β = 90.00
c = 146.535γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance