2GEZ

Crystal structure of potassium-independent plant asparaginase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of plant asparaginase.

Michalska, K.Bujacz, G.Jaskolski, M.

(2006) J.Mol.Biol. 360: 105-116

  • DOI: 10.1016/j.jmb.2006.04.066
  • Also Cited By: 3C17, 2ZAK

  • PubMed Abstract: 
  • In plants, specialized enzymes are required to catalyze the release of ammonia from asparagine, which is the main nitrogen-relocation molecule in these organisms. In addition, K+-independent plant asparaginases are also active in splitting the aberra ...

    In plants, specialized enzymes are required to catalyze the release of ammonia from asparagine, which is the main nitrogen-relocation molecule in these organisms. In addition, K+-independent plant asparaginases are also active in splitting the aberrant isoaspartyl peptide bonds, which makes these proteins important for seed viability and germination. Here, we present the crystal structure of potassium-independent L-asparaginase from yellow lupine (LlA) and confirm the classification of this group of enzymes in the family of Ntn-hydrolases. The alpha- and beta-subunits that form the mature (alphabeta)2 enzyme arise from autoproteolytic cleavage of two copies of a precursor protein. In common with other Ntn-hydrolases, the (alphabeta) heterodimer has a sandwich-like fold with two beta-sheets flanked by two layers of alpha-helices (alphabetabetaalpha). The nucleophilic Thr193 residue, which is liberated in the autocatalytic event at the N terminus of subunit beta, is part of an active site that is similar to that observed in a homologous bacterial enzyme. An unusual sodium-binding loop of the bacterial protein, necessary for proper positioning of all components of the active site, shows strictly conserved conformation and metal coordination in the plant enzyme. A chloride anion complexed in the LlA structure marks the position of the alpha-carboxylate group of the L-aspartyl substrate/product moiety. Detailed analysis of the active site suggests why the plant enzyme hydrolyzes asparagine and its beta-peptides but is inactive towards substrates accepted by similar Ntn-hydrolases, such as taspase1, an enzyme implicated in some human leukemias. Structural comparisons of LlA and taspase1 provide interesting insights into the role of small inorganic ions in the latter enzyme.


    Related Citations: 
    • Expression, purification and catalytic activity of Lupinus luteus asparagine beta-amidohydrolase and its Escherichia coli homolog.
      Borek, D.,Michalska, K.,Brzezinski, K.,Kisiel, A.,Podkowinski, J.,Bonthron, T.D.,Krowarsch, D.,Otlewski, J.,Jaskolski, M.
      (2004) Eur.J.Biochem. 271: 3215
    • Structure of the isoaspartyl peptidase with L-asparaginase activity from Escherichia coli.
      Prahl, A.,Pazgier, M.,Hejazi, M.,Lockau, W.,Lubkowski, J.
      (2004) Acta Crystallogr.,Sect.D 60: 1173
    • Crystal structure of isoaspartyl aminopeptidase in complex with L-aspartate.
      Michalska, K.,Brzezinski, K.,Jaskolski, M.
      (2005) J.Biol.Chem. 280: 28491
    • Crystallization and preliminary crystallographic studies of a new L-asparaginase encoded by the Escherichia coli genome.
      Borek, D.,Jaskolski, M.
      (2000) Acta Crystallogr.,Sect.D 56: 1505
    • Three-dimensional structure of human lysosomal aspartylglucosaminidase.
      Oinonen, C.,Tikkanen, R.,Rouvinen, J.,Peltonen, L.
      (1995) Nat.Struct.Mol.Biol. 2: 1102
    • Crystal structure of human Taspase1, a crucial protease regulating the function of MLL.
      Khan, J.A.,Dunn, B.M.,Tong, L.
      (2005) Structure 13: 1443
    • Crystal structures of Flavobacterium glycosylasparaginase. An N-terminal nucleophile hydrolase activated by intramolecular proteolysis.
      Guo, H.C.,Xu, Q.,Buckley, D.,Guan, C.
      (1998) J.Biol.Chem. 273: 20205
    • A protein catalytic framework with an N-terminal nucleophile is capable of self-activation.
      Brannigan, J.A.,Dodson, G.,Duggleby, H.J.,Moody, P.C.,Smith, J.L.,Tomchick, D.R.,Murzin, A.G.
      (1995) Nature 378: 416


    Organizational Affiliation

    Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-asparaginase alpha subunit
A, C, E, G
195Lupinus luteusMutation(s): 0 
EC: 3.4.19.5
Find proteins for Q9ZSD6 (Lupinus luteus)
Go to UniProtKB:  Q9ZSD6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
L-asparaginase beta subunit
B, D, F, H
133Lupinus luteusMutation(s): 0 
EC: 3.4.19.5
Find proteins for Q9ZSD6 (Lupinus luteus)
Go to UniProtKB:  Q9ZSD6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, C, E, G
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B, D, F, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.189 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 47.680α = 100.60
b = 60.200β = 92.90
c = 114.630γ = 113.40
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance