9BAD | pdb_00009bad

Crystal structure of Bacillus subtilis 168 L-asparaginase II with antileukemic activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.164 (Depositor), 0.167 (DCC) 
  • R-Value Work: 
    0.136 (Depositor), 0.139 (DCC) 
  • R-Value Observed: 
    0.137 (Depositor) 

Starting Model: in silico
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This is version 1.2 of the entry. See complete history


Literature

Structural and biochemical characterization of a thermostable Bacillus subtilis L-asparaginase with antiproliferative effects on hematological cancer cell lines.

Brandao, L.C.da Silva Gomes, J.G.Pinheiro, D.P.Caetano, L.F.Bezerra, M.R.L.Pontes, L.Q.Pinheiro, M.P.de Aquino, A.V.F.G.Silva, J.M.F.Souza, P.F.N.Furtado, C.L.M.Pessoa, C.Lourenzoni, M.R.da Rocha, B.A.M.Furtado, G.P.

(2025) Int J Biol Macromol 333: 148804-148804

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.148804
  • Primary Citation of Related Structures:  
    9BAD

  • PubMed Abstract: 

    L-asparaginase catalyzes the hydrolysis of L-asparagine into aspartic acid and ammonia and is found in animals, plants, and microorganisms. Microbial sources are preferred for large-scale production due to their efficiency and ease of cultivation. In this study, we produced and characterized a recombinant L-asparaginase from Bacillus subtilis (Asp-Z). Asp-Z was heterologously expressed in Escherichia coli and purified by affinity chromatography, yielding soluble protein with optimal activity at 55 °C and pH 7.5. The kinetic parameters under these conditions were a Km of 0.47 mM and a Vmax of 52.13 U/mg. Asp-Z was specific for L-asparagine, showing no detectable glutaminase activity, and exhibited antiproliferative effects against hematological cancer cell lines, particularly RAJI and JURKAT, with IC₅₀ values in the micromolar range. In silico analysis revealed distinct immunogenic epitopes between Asp-Z and the commercial E. coli L-asparaginase, suggesting divergent antigenic profiles, whereas crystallographic data revealed a conserved tetrameric fold with a highly flexible active-site loop. Together, these findings highlight Asp-Z as a thermostable, glutaminase-free, and poorly immunogenic enzyme that represents a promising scaffold for optimization through protein engineering toward therapeutic and biotechnological applications.


  • Organizational Affiliation
    • Protein Engineering and Health Solutions Group (GEPeSS), Oswaldo Cruz Foundation (Fiocruz), Eusébio, Ceará, Brazil; Graduate Program in Biotechnology of Natural Resources (PPGBiotec), Department of Fisheries Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-asparaginase 2
A, B, C, D
375Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: ansZyccCBSU02690
EC: 3.5.1.1
UniProt
Find proteins for O34482 (Bacillus subtilis (strain 168))
Explore O34482 
Go to UniProtKB:  O34482
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34482
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.164 (Depositor), 0.167 (DCC) 
  • R-Value Work:  0.136 (Depositor), 0.139 (DCC) 
  • R-Value Observed: 0.137 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.234α = 90
b = 104.486β = 90
c = 123.055γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil313837/2020-1

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Database references
  • Version 1.2: 2025-11-26
    Changes: Database references