3ECA

CRYSTAL STRUCTURE OF ESCHERICHIA COLI L-ASPARAGINASE, AN ENZYME USED IN CANCER THERAPY (ELSPAR)

• PDB DOI: https://doi.org/10.2210/pdb3ECA/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1993-07-02 Released: 1993-10-31 
• Deposition Author(s): Swain, A.L., Jaskolski, M., Housset, D., Rao, J.K.M., Wlodawer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 0.111 
• R-Value Observed: 0.111 

Literature

Crystal structure of Escherichia coli L-asparaginase, an enzyme used in cancer therapy.

Swain, A.L., Jaskolski, M., Housset, D., Rao, J.K., Wlodawer, A.

(1993) Proc Natl Acad Sci U S A 90: 1474-1478

• PubMed: 8434007 
• DOI: https://doi.org/10.1073/pnas.90.4.1474
• Primary Citation of Related Structures:  
  3ECA


• PubMed Abstract: 
  

  The crystal structure of Escherichia coli asparaginase II (EC 3.5.1.1), a drug (Elspar) used for the treatment of acute lymphoblastic leukemia, has been determined at 2.3 A resolution by using data from a single heavy atom derivative in combination with molecular replacement. The atomic model was refined to an R factor of 0.143. This enzyme, active as a homotetramer with 222 symmetry, belongs to the class of alpha/beta proteins. Each subunit has two domains with unique topological features. On the basis of present structural evidence consistent with previous biochemical studies, we propose locations for the active sites between the N- and C-terminal domains belonging to different subunits and postulate a catalytic role for Thr-89.

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Organizational Affiliation: 

Macromolecular Structure Laboratory, National Cancer Institute-Frederick Cancer Research and Development Center, MD 21702-1201.

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: 139.04 kDa 
• Atom Count: 10,225 
• 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-asparaginase 2	A, B, C, D	326	Escherichia coli	Mutation(s): 0  EC: 3.5.1.1
UniProt
Find proteins for P00805 (Escherichia coli (strain K12)) Explore P00805  Go to UniProtKB:  P00805

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ASP	E [auth A], F [auth B], G [auth C], H [auth D]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 0.111 
• R-Value Observed: 0.111 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.7	α = 90
b = 96.1	β = 97.1
c = 111.3	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
X-PLOR	model building
X-PLOR	phasing
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Swain, A.L., Jaskolski, M., Housset, D., Rao, J.K.M., Wlodawer, A.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 2.0: 2020-07-29
  Type: Coordinate replacement
  Reason: Sequence discrepancy
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary