Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 67138.73 
• Atom Count: 4303 
• Residue Count: 640 
• Unique protein chains: 2

1K2X

Crystal structure of putative asparaginase encoded by Escherichia coli ybiK gene

• DOI: 10.2210/pdb1K2X/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli


• Deposited: 2001-09-30 Released: 2003-09-09 
• Deposition Author(s): Borek, D., Jaskolski, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.198 
• R-Value Work: 0.163 

Literature

Crystal packing of plant-type L-asparaginase from Escherichia coli.

Michalska, K., Borek, D., Hernandez-Santoyo, A., Jaskolski, M.

(2008) Acta Crystallogr.,Sect.D 64: 309-320

• PubMed: 18323626 
• DOI: 10.1107/S0907444907068072
• Primary Citation of Related Structures:  
  2ZAK, 1JN9


• PubMed Abstract: 
  

Plant-type L-asparaginases hydrolyze the side-chain amide bond of L-asparagine or its beta-peptides. They belong to the N-terminal nucleophile (Ntn) hydrolases and are synthesized as inactive precursor molecules. Activation occurs via the autoproteolytic release of two subunits, alpha and beta, the latter of which carries the nucleophile at its N-terminus. Crystallographic studies of plant-type asparaginases have focused on an Escherichia coli homologue (EcAIII), which has been crystallized in several crystal forms. Although they all belong to the same P2 1 2 1 2 1 space group with similar unit-cell parameters, they display different crystal-packing arrangements and thus should be classified as separate polymorphs. This variability stems mainly from different positions of the EcAIII molecules within the unit cell, although they also exhibit slight differences in orientation. The intermolecular interactions that trigger different crystal lattice formation are mediated by ions, which represent the most variable component of the crystallization conditions. This behaviour confirms recent observations that small molecules might promote protein crystal lattice formation.

---

Related Citations: 

• Structural Insights into the Mechanism of Intramolecular Proteolysis
  Xu, Q.,Buckley, D.,Guan, C.,Guo, H.C.
  (1999) Cell 98: 651
• Crystal Structures of Flavobacterium Glycosylasparaginase. An N-terminal Nucleophile Hydrolase Activated by Intramolecular Proteolysis
  Guo, H.C.,Xu, Q.,Buckley, D.,Guan, C.
  (1998) J.Biol.Chem. 273: 20205
• Crystallization and Preliminary Crystallographic Studies of a New L-asparaginase Encoded by the Escherichia coli Genome
  Borek, D.,Jaskolski, M.
  (2000) Acta Crystallogr.,Sect.D 56: 1505
• A Protein Catalytic Framework with an N-terminal Nucleophile is Capable of Self-activation
  Brannigan, J.A.,Dodson, G.,Duggleby, H.J.,Moody, P.C.,Smith, J.L.,Tomchick, D.R.,Murzin, A.G.
  (1995) Nature 378: 416
• Three-dimensional Structure of Human Lysosomal Aspartylglucosaminidase
  Oinonen, C.,Tikkanen, R.,Rouvinen, J.,Peltonen, L.
  (1995) Nat.Struct.Mol.Biol. 2: 1102
• Crystal Structure of Glycosylasparaginase from Flavobacterium Meningosepticum
  Xuan, J.,Tarentino, A.L.,Grimwood, B.G.,Plummer Jr., T.H.,Cui, T.,Guan, C.,Van Roey, P.
  (1998) Protein Sci. 7: 774




---

Organizational Affiliation: 

Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Putative L-asparaginase	A, C	177	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: iaaA (spt, ybiK) EC: 3.4.19.5
Find proteins for P37595 (Escherichia coli (strain K12)) Go to UniProtKB:  P37595

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Putative L-asparaginase	B, D	143	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: iaaA (spt, ybiK) EC: 3.4.19.5
Find proteins for P37595 (Escherichia coli (strain K12)) Go to UniProtKB:  P37595

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A, C	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
CL	A, C, D	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, C	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.198 
• R-Value Work: 0.163 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 50.296	α = 90.00
b = 77.624	β = 90.00
c = 148.152	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
EPMR	phasing
DENZO	data reduction
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-09-30 
• Released Date: 2003-09-09 
• Deposition Author(s): Borek, D., Jaskolski, M.

Revision History 

• Version 1.0: 2003-09-09
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Derived calculations, Version format compliance