2ZAK

Orthorhombic crystal structure of precursor E. coli isoaspartyl peptidase/L-asparaginase (EcAIII) with active-site T179A mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1107/S0907444907068072
  • Primary Citation of Related Structures:  

  • 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 autoproteol ...

    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: 
    • Crystal structure of plant asparaginase
      Michalska, K.,Bujacz, G.,Jaskolski, M.
      (2006) J.Mol.Biol. 360: 105
    • 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
    • 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.,Sect.D 60: 1173
    • 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
    • A dual role for an aspartic acid in glycosylasparaginase autoproteolysis
      Qian, X.,Guan, C.,Guo, H.-C.
      (2003) Structure 11: 997
    • Structural insights into the mechanism of intramolecular proteolysis
      Xu, Q.,Buckley, D.,Guan, C.,Guo, H.-C.
      (1999) Cell 98: 651
    • 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
    • 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.,Sect.D 56: 1505


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-asparaginase precursor
A, B
320Escherichia coli (strain K12)Mutation(s): 1 
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.350α = 90.00
b = 77.780β = 90.00
c = 147.930γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance