7QY6

Structure of E.coli Class 2 L-asparaginase EcAIII, wild type (WT EcAIII)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and biophysical studies of new L-asparaginase variants: lessons from random mutagenesis of the prototypic Escherichia coli Ntn-amidohydrolase.

Loch, J.I.Klonecka, A.Kadziolka, K.Bonarek, P.Barciszewski, J.Imiolczyk, B.Brzezinski, K.Gilski, M.Jaskolski, M.

(2022) Acta Crystallogr D Struct Biol 78: 911-926

  • DOI: https://doi.org/10.1107/S2059798322005691
  • Primary Citation of Related Structures:  
    7QQ8, 7QSF, 7QTC, 7QVR, 7QY6, 7QYM, 7QYX, 7R1G, 7R5C

  • PubMed Abstract: 

    This work reports the results of random mutagenesis of the Escherichia coli class 2 L-asparaginase EcAIII belonging to the Ntn-hydrolase family. New variants of EcAIII were studied using structural, biophysical and bioinformatic methods. Activity tests revealed that the L-asparaginase activity is abolished in all analyzed mutants with the absence of Arg207, but some of them retained the ability to undergo the autoproteolytic maturation process. The results of spectroscopic studies and the determined crystal structures showed that the EcAIII fold is flexible enough to accept different types of mutations; however, these mutations may have a diverse impact on the thermal stability of the protein. The conclusions from the experiments are grouped into six lessons focused on (i) the adaptation of the EcAIII fold to new substitutions, (ii) the role of Arg207 in EcAIII activity, (iii) a network of residues necessary for autoprocessing, (iv) the complexity of the autoprocessing reaction, (v) the conformational changes observed in enzymatically inactive variants and (vi) the cooperativity of the EcAIII dimer subunits. Additionally, the structural requirements (pre-maturation checkpoints) that are necessary for the initiation of the autocleavage of Ntn-hydrolases have been classified. The findings reported in this work provide useful hints that should be considered before planning enzyme-engineering experiments aimed at the design of proteins for therapeutic applications. This is especially important for L-asparaginases that can be utilized in leukemia therapy, as alternative therapeutics are urgently needed to circumvent the severe side effects associated with the currently used enzymes.


  • Organizational Affiliation

    Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Krakow, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoaspartyl peptidaseA [auth AAA],
C [auth CCC]
178Escherichia coliMutation(s): 0 
Gene Names: iaaAsptybiKb0828JW0812
EC: 3.4.19.5
UniProt
Find proteins for P37595 (Escherichia coli (strain K12))
Explore P37595 
Go to UniProtKB:  P37595
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37595
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-aspartyl-peptidaseB [auth BBB],
D [auth DDD]
143Escherichia coliMutation(s): 0 
Gene Names: iaaAHLZ50_00315
EC: 3.4.19.5
UniProt
Find proteins for A0A246NXR9 (Escherichia coli)
Explore A0A246NXR9 
Go to UniProtKB:  A0A246NXR9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A246NXR9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.478α = 90
b = 75.347β = 90
c = 147.991γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2020/38/E/NZ1/00035

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description