3C17 | pdb_00003c17

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 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 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 Biological Chem 283: 13388-13397

  • DOI: https://doi.org/10.1074/jbc.M800746200
  • Primary Citation 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. 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.


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

Macromolecule Content 

  • Total Structure Weight: 67.38 kDa 
  • Atom Count: 4,968 
  • Modeled Residue Count: 611 
  • Deposited Residue Count: 640 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
L-asparaginase precursor
A, B
320Escherichia coli K-12Mutation(s): 1 
Gene Names: ybiK (iaaA)
EC: 3.4.19.5 (PDB Primary Data), 3.5.1.1 (PDB Primary Data)
UniProt
Find proteins for P37595 (Escherichia coli (strain K12))
Explore P37595 
Go to UniProtKB:  P37595
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37595
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / 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]
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
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.203 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
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

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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
  • Version 1.2: 2021-11-10
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description