2ZAL

Crystal structure of E. coli isoaspartyl aminopeptidase/L-asparaginase in complex with L-aspartate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of isoaspartyl aminopeptidase in complex with L-aspartate

Michalska, K.Brzezinski, K.Jaskolski, M.

(2005) J Biol Chem 280: 28484-28491

  • DOI: 10.1074/jbc.M504501200
  • Primary Citation of Related Structures:  
    2ZAL

  • PubMed Abstract: 
  • The crystal structure of Escherichia coli isoaspartyl aminopeptidase/asparaginase (EcAIII), an enzyme belonging to the N-terminal nucleophile (Ntn)-hydrolases family, has been determined at 1.9-A resolution for a complex obtained by cocrystallization with l-aspartate, which is a product of both enzymatic reactions catalyzed by EcAIII ...

    The crystal structure of Escherichia coli isoaspartyl aminopeptidase/asparaginase (EcAIII), an enzyme belonging to the N-terminal nucleophile (Ntn)-hydrolases family, has been determined at 1.9-A resolution for a complex obtained by cocrystallization with l-aspartate, which is a product of both enzymatic reactions catalyzed by EcAIII. The enzyme is a dimer of heterodimers, (alphabeta)(2). The (alphabeta) heterodimer, which arises by autoproteolytic cleavage of the immature protein, exhibits an alphabetabetaalpha-sandwich fold, typical for Ntn-hydrolases. The asymmetric unit contains one copy of the EcAIII.Asp complex, with clearly visible l-aspartate ligands, one bound in each of the two active sites of the enzyme. The l-aspartate ligand is located near Thr(179), the N-terminal residue of subunit beta liberated in the autoproteolytic event. Structural comparisons with the free form of EcAIII reveal that there are no major rearrangements of the active site upon aspartate binding. Although the ligand binding mode is similar to that observed in an l-aspartate complex of the related enzyme human aspartylglucosaminidase, the architecture of the EcAIII active site sheds light on the question of substrate specificity and explains why EcAIII is not able to hydrolyze glycosylated asparagine substrates.


    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.E., 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 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
    • Autoproteolytic activation of human aspartylglucosaminidase
      Saarela, J., Oinonen, C., Jalanko, A., Rouvinen, J., Peltonen, L.
      (2004) Biochem J 378: 363
    • 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 D Biol Crystallogr 60: 1173

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-asparaginaseA, C160Escherichia coli K-12Mutation(s): 0 
Gene Names: ybiK (iaaA)iaaAsptybiKb0828JW0812
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
L-asparaginaseB, D137Escherichia coli K-12Mutation(s): 0 
Gene Names: ybiK (iaaA)iaaAsptybiKb0828JW0812
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ASP
Query on ASP

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
M [auth B],
N [auth B],
S [auth D]
ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
Q [auth C],
R [auth C]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
P [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
O [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.89α = 90
b = 77.28β = 90
c = 147.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2018-05-23
    Changes: Data collection