3O98

Glutathionylspermidine synthetase/amidase C59A complex with ADP and Gsp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.220 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structure and mechanism of Escherichia coli glutathionylspermidine amidase belonging to the family of cysteine; histidine-dependent amidohydrolases/peptidases

Pai, C.-H.Wu, H.-J.Lin, C.-H.Wang, A.H.-J.

(2011) Protein Sci 20: 557-566

  • DOI: https://doi.org/10.1002/pro.589
  • Primary Citation of Related Structures:  
    3A2Y, 3O98

  • PubMed Abstract: 

    The bifunctional Escherichia coli glutathionylspermidine synthetase/amidase (GspSA) catalyzes both the synthesis and hydrolysis of Gsp. Its amidase domain (GspA), which catalyzes the hydrolysis of Gsp into glutathione and spermidine, plays an important role in redox sensing and protein S-thiolation. To gain insight of the regulation and catalytic mechanism of and further understand the recycling of the Gsp dimer and Gsp-S-protein adducts, we solved two crystal structures of GspA and GspSA both with the C59A mutation and bound with the substrate, Gsp. In both structures, Cys59, His131, and Glu147 form the catalytic triad, which is similar to other cysteine proteases. Comparison of the GspA_Gsp complex and apo GspSA structures indicates that on binding with Gsp, the side chains of Asn149 and Gln58 of the amidase domain are induced to move closer to the carbonyl oxygen of the cleaved amide bond of Gsp, thereby participating in catalysis. In addition, the helix-loop region of GspA, corresponding to the sequence (30)YSSLDPQEYEDDA(42), involves in regulating the substrate binding. Our previous study indicated that the thiol of Cys59 of GspA is only oxidized to sulfenic acid by H(2)O(2). When comparing the active site of GspA with those of other cysteine proteases, we found that limited space and hydrophobicity of the environment around Cys59 play an important role to inhibit its further oxidation. The structural results presented here not only elucidate the catalytic mechanism and regulation of GspA but also help us to design small molecules to inhibit or probe for the activity of GspA.


  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional glutathionylspermidine synthetase/amidase
A, B
619Escherichia coli K-12Mutation(s): 1 
EC: 6.3.1.8 (PDB Primary Data), 3.5.1.78 (PDB Primary Data)
UniProt
Find proteins for P0AES0 (Escherichia coli (strain K12))
Explore P0AES0 
Go to UniProtKB:  P0AES0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AES0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.220 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.38α = 70.81
b = 76.2β = 74.37
c = 84.22γ = 78.64
Software Package:
Software NamePurpose
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-12-07
    Changes: Advisory, Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description