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 
  • R-Value Observed: 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 D Biol Crystallogr 64: 309-320

  • DOI: 10.1107/S0907444907068072
  • Primary Citation of Related Structures:  
    2ZAK, 1JN9, 1K2X

  • 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: 
    • 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
    • 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
    • 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
    • Three-dimensional Structure of Human Lysosomal Aspartylglucosaminidase
      Oinonen, C., Tikkanen, R., Rouvinen, J., Peltonen, L.
      (1995) Nat Struct Mol Biol 2: 1102
    • 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
    • Structural Insights into the Mechanism of Intramolecular Proteolysis
      Xu, Q., Buckley, D., Guan, C., Guo, H.C.
      (1999) Cell 98: 651

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative L-asparaginaseAC177Escherichia coliMutation(s): 1 
Gene Names: ybiK
EC: 3.5.1.1 (PDB Primary Data), 3.4.19.5 (UniProt)
Find proteins for P37595 (Escherichia coli (strain K12))
Explore P37595 
Go to UniProtKB:  P37595
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Putative L-asparaginaseBD143Escherichia coliMutation(s): 0 
Gene Names: ybiK
EC: 3.5.1.1 (PDB Primary Data), 3.4.19.5 (UniProt)
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 CCD File 
A, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A,CL-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 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.296α = 90
b = 77.624β = 90
c = 148.152γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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