1T3M

Structure of the isoaspartyl peptidase with L-asparaginase activity from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 1173-1176

  • DOI: 10.1107/S0907444904003403
  • Also Cited By: 2ZAL, 3C17, 2ZAK

  • PubMed Abstract: 
  • The crystal structure of the Escherichia coli enzyme (EcAIII) with isoaspartyl dipeptidase and L-asparaginase activity has been solved and refined to a resolution of 1.65 angstroms, with crystallographic R-factor and Rfree values of 0.178 and 0.209, ...

    The crystal structure of the Escherichia coli enzyme (EcAIII) with isoaspartyl dipeptidase and L-asparaginase activity has been solved and refined to a resolution of 1.65 angstroms, with crystallographic R-factor and Rfree values of 0.178 and 0.209, respectively. EcAIII belongs to the family of N-terminal hydrolases. The amino-acid sequence of EcAIII is homologous to those of putative asparaginases from plants. The structure of EcAIII is similar to the structures of glycosylasparaginases. The mature and catalytically active form of EcAIII is a heterotetramer consisting of two alpha-subunits and two beta-subunits. Both of the equivalent active sites present in the EcAIII tetramer is assisted by a metal-binding site. The metal cations, modelled here as Na+, have not previously been observed in glycosylasparaginases. This reported structure helps to explain the inability of EcAIII and other plant-type asparaginases to hydrolyze N4-(beta-N-acetylglucosaminyl)-L-asparagine, the substrate of glycosylasparaginases.


    Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative L-asparaginase
A, C
177Escherichia coli (strain K12)Mutation(s): 0 
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
147Escherichia coli (strain K12)Mutation(s): 0 
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
NO3
Query on NO3

Download SDF File 
Download CCD File 
A, B, C
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.318α = 90.00
b = 71.637β = 90.00
c = 149.583γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
HKL-2000data reduction
SHELXL-97refinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance