Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 67.38 kDa 
• Atom Count: 4968 
• Modelled Residue Count: 611 
• Deposited Residue Count: 640 
• Unique protein chains: 1

3C17

Hexagonal Crystal Structure of Precursor E. coli Isoaspartyl Peptidase/l-Asparaginase (ECAIII) with Active-site T179A mutation

• PDB DOI: 10.2210/pdb3C17/pdb

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


• Deposited: 2008-01-22 Released: 2008-04-01 
• Deposition Author(s): Michalska, K., Hernandez-Santoyo, A., Jaskolski, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.203 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

Literature

The Mechanism of Autocatalytic Activation of Plant-type L-Asparaginases

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

(2008) J Biol Chem 283: 13388-13397

• PubMed: 18334484 
• DOI: 10.1074/jbc.M800746200
• Primary Citation of Related Structures:  
  3C17


• PubMed Abstract: 
  

Plant l-asparaginases and their bacterial homologs, such as EcAIII found in Escherichia coli, form a subgroup of the N-terminal nucleophile (Ntn)-hydrolase family. In common with all Ntn-hydrolases, they are expressed as inactive precursors that undergo activation in an autocatalytic manner. The maturation process involves intramolecular hydrolysis of a single peptide bond, leading to the formation of two subunits (alpha and beta) folded as one structural domain, with the nucleophilic Thr residue located at the freed N terminus of subunit beta. The mechanism of the autocleavage reaction remains obscure. We have determined the crystal structure of an active site mutant of EcAIII, with the catalytic Thr residue substituted by Ala (T179A). The modification has led to a correctly folded but unprocessed molecule, revealing the geometry and molecular environment of the scissile peptide bond. The autocatalytic reaction is analyzed from the point of view of the Thr(179) side chain rotation, identification of a potential general base residue, and the architecture of the oxyanion hole.

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Related Citations: 

• Crystal packing of plant-type L-asparaginase from Escherichia coli
  Michalska, K., Borek, D., Hernandez-Santoyo, A., Jaskolski, M.
  () To be published --: --

• Crystal structure of isoaspartyl aminopeptidase in complex with L-aspartate
  Michalska, K., Brzezinski, K., Jaskolski, M.
  (2005) J Biol Chem 280: 28484

• Crystallization and preliminary crystallographic studies of a new L-asparaginase encoded by the Escherichia coli genome
  Borek, D., Jaskolski, M.
  (2000) Acta Crystallogr D Biol Crystallogr 56: 1505

• Crystal structure of plant asparaginase
  Michalska, K., Bujacz, G., Jaskolski, M.
  (2006) J Mol Biol 360: 105

• Structure of the isoaspartyl peptidase with L-asparaginase activity from Escherichia coli
  Prahl, A., Pazgier, M., Hejazi, M., Lockau, W., Lubkowski, J.
  (2004) Acta Crystallogr D Biol Crystallogr 60: 1173

• Structural insights into the mechanism of intramolecular proteolysis
  Xu, Q., Buckley, D., Guan, C., Guo, H.-C.
  (1999) Cell 98: 651

• Characterization and functional analysis of the cis-autoproteolysis active center of glycosylasparaginase
  Guan, C., Liu, Y., Shao, Y., Cui, T., Liao, W., Ewel, A., Whitaker, R., Paulus, H.
  (1998) J Biol Chem 273: 9695

• Activation and oligomerization of aspartylglucosaminidase
  Saarela, J., Laine, M., Tikkanen, R., Oinonen, C., Jalanko, A., Rouvinen, J., Peltonen, L.
  (1998) J Biol Chem 273: 25320

• A dual role for an aspartic acid in glycosylasparaginase autoproteolysis
  Qian, X., Guan, C., Guo, H.-C.
  (2003) Structure 11: 997

• 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

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Organizational Affiliation: 

Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan 60-780, Poland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase precursor	A, B	320	Escherichia coli K-12	Mutation(s): 1  Gene Names: ybiK (iaaA), iaaA, spt, ybiK, b0828, JW0812 EC: 3.4.19.5 (PDB Primary Data), 3.5.1.1 (PDB Primary Data)
UniProt
Find proteins for P37595 (Escherichia coli (strain K12)) Explore P37595  Go to UniProtKB:  P37595

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	AA [auth B], BA [auth B], CA [auth B], DA [auth B], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.203 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.47	α = 90
b = 149.47	β = 90
c = 214.35	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-22 
• Released Date: 2008-04-01 
Deposition Author(s): Michalska, K., Hernandez-Santoyo, A., Jaskolski, M.

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2021-11-10
  Changes: Data collection, Database references, Derived calculations