4PV2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1107/S1399004714008700
  • Primary Citation of Related Structures:  
    4PU6, 4PV2, 4PV3

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-ASPARAGINASE ALPHA SUBUNIT
A, C
197Phaseolus vulgarisMutation(s): 0 
Gene Names: PHAVU_001G025000g
EC: 3.5.1.1
UniProt
Find proteins for V7CU13 (Phaseolus vulgaris)
Explore V7CU13 
Go to UniProtKB:  V7CU13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV7CU13
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
L-ASPARAGINASE BETA SUBUNIT
B, D
131Phaseolus vulgarisMutation(s): 0 
Gene Names: PHAVU_001G025000g
EC: 3.5.1.1
UniProt
Find proteins for V7CU13 (Phaseolus vulgaris)
Explore V7CU13 
Go to UniProtKB:  V7CU13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV7CU13
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth D]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
Q [auth C],
R [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
O [auth C],
P [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.885α = 90
b = 102.632β = 90
c = 123.754γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description