The thermostable L-asparaginase from Thermococcus kodakarensis

Experimental Data Snapshot

  • Resolution: 2.18 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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Structure and function of the thermostable L-asparaginase from Thermococcus kodakarensis.

Guo, J.Coker, A.R.Wood, S.P.Cooper, J.B.Chohan, S.M.Rashid, N.Akhtar, M.

(2017) Acta Crystallogr D Struct Biol 73: 889-895

  • DOI: https://doi.org/10.1107/S2059798317014711
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    L-Asparaginases catalyse the hydrolysis of asparagine to aspartic acid and ammonia. In addition, L-asparaginase is involved in the biosynthesis of amino acids such as lysine, methionine and threonine. These enzymes have been used as chemotherapeutic agents for the treatment of acute lymphoblastic leukaemia and other haematopoietic malignancies since the tumour cells cannot synthesize sufficient L-asparagine and are thus killed by deprivation of this amino acid. L-Asparaginases are also used in the food industry and have potential in the development of biosensors, for example for asparagine levels in leukaemia. The thermostable type I L-asparaginase from Thermococcus kodakarensis (TkA) is composed of 328 amino acids and forms homodimers in solution, with the highest catalytic activity being observed at pH 9.5 and 85°C. It has a K m value of 5.5 mM for L-asparagine, with no glutaminase activity being observed. The crystal structure of TkA has been determined at 2.18 Å resolution, confirming the presence of two α/β domains connected by a short linker region. The N-terminal domain contains a highly flexible β-hairpin which adopts `open' and `closed' conformations in different subunits of the solved TkA structure. In previously solved L-asparaginase structures this β-hairpin was only visible when in the `closed' conformation, whilst it is characterized with good electron density in all of the subunits of the TkA structure. A phosphate anion resides at the active site, which is formed by residues from both of the neighbouring monomers in the dimer. The high thermostability of TkA is attributed to the high arginine and salt-bridge content when compared with related mesophilic enzymes.

  • Organizational Affiliation

    School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
328Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK1656
Find proteins for Q5JIW4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JIW4 
Go to UniProtKB:  Q5JIW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JIW4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PG4

Download Ideal Coordinates CCD File 
C8 H18 O5
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
M [auth C]
N [auth D]
Q [auth E]
G [auth A],
I [auth B],
M [auth C],
N [auth D],
Q [auth E],
R [auth F]
O4 P
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
K [auth B]
O [auth D]
P [auth D]
H [auth A],
J [auth B],
K [auth B],
O [auth D],
P [auth D],
S [auth F]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.18 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.74α = 72.13
b = 70.96β = 76.22
c = 107.73γ = 87.83
Software Package:
Software NamePurpose
Cootmodel building
xia2data reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-08
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references