3C17

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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.


    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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-asparaginase precursorA, B320Escherichia coli K-12Mutation(s): 1 
Gene Names: ybiK (iaaA)iaaAsptybiKb0828JW0812
EC: 3.4.19.5 (PDB Primary Data), 3.5.1.1 (PDB Primary Data)
Find proteins for P37595 (Escherichia coli (strain K12))
Explore P37595 
Go to UniProtKB:  P37595
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , CA [auth B] , DA [auth B] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , 
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
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , Q [auth B] , R [auth B] , S [auth B] , 
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
 Ligand Interaction
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 = 149.47α = 90
b = 149.47β = 90
c = 214.35γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance