4ECA

ASPARAGINASE FROM E. COLI, MUTANT T89V WITH COVALENTLY BOUND ASPARTATE

• PDB DOI: https://doi.org/10.2210/pdb4ECA/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1997-02-21 Released: 1997-06-16 
• Deposition Author(s): Palm, G.J., Lubkowski, J., Wlodawer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.181 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

A covalently bound catalytic intermediate in Escherichia coli asparaginase: crystal structure of a Thr-89-Val mutant.

Palm, G.J., Lubkowski, J., Derst, C., Schleper, S., Rohm, K.H., Wlodawer, A.

(1996) FEBS Lett 390: 211-216

• PubMed: 8706862 
• DOI: https://doi.org/10.1016/0014-5793(96)00660-6
• Primary Citation of Related Structures:  
  4ECA


• PubMed Abstract: 
  

  Escherichia coli asparaginase II catalyzes the hydrolysis of L-asparagine to L-aspartate via a threonine-bound acyl-enzyme intermediate. A nearly inactive mutant in which one of the active site threonines, Thr-89, was replaced by valine was constructed, expressed, and crystallized. Its structure, solved at 2.2 A resolution, shows high overall similarity to the wild-type enzyme, but an aspartyl moiety is covalently bound to Thr-12, resembling a reaction intermediate. Kinetic analysis confirms the deacylation deficiency, which is also explained on a structural basis. The previously identified oxyanion hole is described in more detail.

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Organizational Affiliation: 

Macromolecular Structure Laboratory, NCI-Frederick Cancer Research and Development Center, Frederick, MD 21702-1201, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 138.96 kDa 
• Atom Count: 10,476 
• Modelled Residue Count: 1,304 
• Deposited Residue Count: 1,304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-ASPARAGINE AMIDOHYDROLASE	A, B, C, D	326	Escherichia coli K-12	Mutation(s): 2  Gene Names: ANSB EC: 3.5.1.1
UniProt
Find proteins for P00805 (Escherichia coli (strain K12)) Explore P00805  Go to UniProtKB:  P00805

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AEI	A, B, C, D	L-PEPTIDE LINKING	C8 H14 N2 O6		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.181 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95	α = 90
b = 126.2	β = 90
c = 155.7	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-06-16 
Deposition Author(s): Palm, G.J., Lubkowski, J., Wlodawer, A.

Revision History  

• Version 1.0: 1997-06-16
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 2.0: 2018-10-03
  Changes: Atomic model, Data collection, Non-polymer description, Structure summary
• Version 2.1: 2021-11-03
  Changes: Database references, Derived calculations
• Version 2.2: 2023-08-09
  Changes: Refinement description