8ECD

E. coli L-asparaginase II mutant (V27T) in complex with L-Asp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.127 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The E. coli L-asparaginase V27T mutant: structural and functional characterization and comparison with theoretical predictions.

Strzelczyk, P.Zhang, D.Wlodawer, A.Lubkowski, J.

(2022) FEBS Lett 596: 3060-3068

  • DOI: https://doi.org/10.1002/1873-3468.14526
  • Primary Citation of Related Structures:  
    8ECD, 8ECE

  • PubMed Abstract: 

    Bacterial L-asparaginases have been used for over 40 years as anticancer drugs. Ardalan et al. (Medical Hypotheses 112, 7-17, 2018) proposed that the V27T mutant of Escherichia coli type II L-asparaginase, EcAII(V27T), should display altered biophysical and catalytic properties compared to the wild-type enzyme, EcAII(wt), rendering it more favourable as a pharmaceutical. They postulated that EcAII(V27T) would exhibit reduced glutaminolytic activity and be more stable compared to EcAII(wt). Their postulates, however, were purely theoretical. Here, we characterized experimentally selected properties of EcAII(V27T). We found asparaginolytic activity of this mutant unchanged, whereas its glutaminolytic activity was fourfold lower compared with EcAII(wt). We did not observe significant differences in stabilities of EcAII(wt) and EcAII(V27T). Crystal structures of the complexes with L-Asp and L-Glu showed considerable differences in binding modes of both substrates.


  • Organizational Affiliation

    Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-asparaginase 2
A, B, C, D
334Escherichia coli K-12Mutation(s): 1 
Gene Names: ansBb2957JW2924
EC: 3.5.1.1
UniProt
Find proteins for P00805 (Escherichia coli (strain K12))
Explore P00805 
Go to UniProtKB:  P00805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00805
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
U [auth C],
V [auth D]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
ASP (Subject of Investigation/LOI)
Query on ASP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C],
W [auth D]
ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D]
CA [auth D]
F [auth A]
J [auth B]
K [auth B]
AA [auth D],
CA [auth D],
F [auth A],
J [auth B],
K [auth B],
N [auth C],
X [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth D]
G [auth A]
H [auth A]
L [auth B]
O [auth C]
BA [auth D],
G [auth A],
H [auth A],
L [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
Y [auth D],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.127 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.559α = 90
b = 62.781β = 117.62
c = 141.052γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary