1K2X

Crystal structure of putative asparaginase encoded by Escherichia coli ybiK gene


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  1JN9, 2ZAK

  • 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: 
    • Three-dimensional Structure of Human Lysosomal Aspartylglucosaminidase
      Oinonen, C.,Tikkanen, R.,Rouvinen, J.,Peltonen, L.
      (1995) Nat.Struct.Mol.Biol. 2: 1102
    • 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
    • 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
    • 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
    • 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, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative L-asparaginase
A, C
177Escherichia coli (strain K12)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
MoleculeChainsSequence LengthOrganismDetails
Putative L-asparaginase
B, D
143Escherichia coli (strain K12)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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

Download SDF File 
Download CCD File 
A, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, C
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
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 = 50.296α = 90.00
b = 77.624β = 90.00
c = 148.152γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
EPMRphasing
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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