4PU6

Crystal structure of potassium-dependent plant-type L-asparaginase from Phaseolus vulgaris in complex with K+ cations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Na+/K+ exchange switches the catalytic apparatus of potassium-dependent plant L-asparaginase

Bejger, M.Imiolczyk, B.Clavel, D.Gilski, M.Pajak, A.Marsolais, F.Jaskolski, M.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1854-1872

  • DOI: 10.1107/S1399004714008700
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Plant-type L-asparaginases, which are a subclass of the Ntn-hydrolase family, are divided into potassium-dependent and potassium-independent enzymes with different substrate preferences. While the potassium-independent enzymes have already been well ...

    Plant-type L-asparaginases, which are a subclass of the Ntn-hydrolase family, are divided into potassium-dependent and potassium-independent enzymes with different substrate preferences. While the potassium-independent enzymes have already been well characterized, there are no structural data for any of the members of the potassium-dependent group to illuminate the intriguing dependence of their catalytic mechanism on alkali-metal cations. Here, three crystal structures of a potassium-dependent plant-type L-asparaginase from Phaseolus vulgaris (PvAspG1) differing in the type of associated alkali metal ions (K(+), Na(+) or both) are presented and the structural consequences of the different ions are correlated with the enzyme activity. As in all plant-type L-asparaginases, immature PvAspG1 is a homodimer of two protein chains, which both undergo autocatalytic cleavage to α and β subunits, thus creating the mature heterotetramer or dimer of heterodimers (αβ)2. The αβ subunits of PvAspG1 are folded similarly to the potassium-independent enzymes, with a sandwich of two β-sheets flanked on each side by a layer of helices. In addition to the `sodium loop' (here referred to as the `stabilization loop') known from potassium-independent plant-type asparaginases, the potassium-dependent PvAspG1 enzyme contains another alkali metal-binding loop (the `activation loop') in subunit α (residues Val111-Ser118). The active site of PvAspG1 is located between these two metal-binding loops and in the immediate neighbourhood of three residues, His117, Arg224 and Glu250, acting as a catalytic switch, which is a novel feature that is identified in plant-type L-asparaginases for the first time. A comparison of the three PvAspG1 structures demonstrates how the metal ion bound in the activation loop influences its conformation, setting the catalytic switch to ON (when K(+) is coordinated) or OFF (when Na(+) is coordinated) to respectively allow or prevent anchoring of the reaction substrate/product in the active site. Moreover, it is proposed that Ser118, the last residue of the activation loop, is involved in the potassium-dependence mechanism. The PvAspG1 structures are discussed in comparison with those of potassium-independent L-asparaginases (LlA, EcAIII and hASNase3) and those of other Ntn-hydrolases (AGA and Tas1), as well as in the light of noncrystallographic studies.


    Related Citations: 
    • Crystal structure of plant asparaginase.
      Michalska, K., Bujacz, G., Jaskolski, M.
      (2006) J Mol Biol 360: 105
    • Crystal structure of isoaspartyl aminopeptidase in complex with L-aspartate
      Michalska, K., Brzezinski, K., Jaskolski, M.
      (2005) J Biol Chem 280: 28484
    • Crystal packing of plant-type L-asparaginase from Escherichia coli
      Michalska, K., Borek, D., Hernandez-Santoyo, A., Jaskolski, M.
      (2008) Acta Crystallogr D Biol Crystallogr D64: 309
    • The mechanism of autocatalytic activation of plant-type L-asparaginases
      Michalska, K., Hernandez-Santoyo, A., Jaskolski, M.
      (2008) J Biol Chem 283: 13388
    • Structural aspects of L-asparaginases, their friends and relations
      Michalska, K., Jaskolski, M.
      (2006) Acta Biochim Pol 53: 627
    • Expression, purification and catalytic activity of Lupinus luteus asparagine -amidohydrolase and its Escherichia coli homolog
      Borek, D., Michalska, K., Brzezinski, K., Kisiel, A., Podkowinski, J., Bonthron, D.T., Krowarsch, D., Otlewski, J., Jaskolski, M.
      (2004) Eur J Biochem 271: 3215
    • Crystallization and preliminary crystallographic studies of a new L-asparaginase encoded by Escherichia coli genome.
      Borek, D., Jaskolski, M.
      (2000) Acta Crystallogr D Biol Crystallogr D56: 1505
    • Sequence analysis of enzymes with asparaginase activity
      Borek, D., Jaskolski, M.
      (2001) Acta Biochim Pol 48: 893
    • Structures of apo and product-bound human L-asparaginase: insights into the mechanism of autoproteolysis and substrate hydrolysis
      Nomme, J., Su, Y., Konrad, M., Lavie, A.
      (2012) Biochemistry 51: 6816
    • Free glicyne accelerates the autoproteolytic activation of human asparaginase
      Su, Y., Karamitros, C.S., Nomme, J., McSorley, T., Konrad, M., Lavie, A.
      (2013) Chem Biol 20: 533

    Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-ASPARAGINASE ALPHA SUBUNIT
A, C
197Phaseolus vulgarisMutation(s): 0 
Gene Names: PHAVU_001G025000g
EC: 3.5.1.1
Find proteins for V7CU13 (Phaseolus vulgaris)
Go to UniProtKB:  V7CU13
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
L-ASPARAGINASE BETA SUBUNIT
B, D
131Phaseolus vulgarisMutation(s): 0 
Gene Names: PHAVU_001G025000g
EC: 3.5.1.1
Find proteins for V7CU13 (Phaseolus vulgaris)
Go to UniProtKB:  V7CU13
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ASP
Query on ASP

Download CCD File 
B
ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.938α = 90
b = 102.672β = 90
c = 127.035γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description