7PVO

Adenylosuccinate Synthetase from H. pylori in complex with IMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The pursuit of new alternative ways to eradicate Helicobacter pylori continues: Detailed characterization of interactions in the adenylosuccinate synthetase active site.

Bubic, A.Narczyk, M.Petek, A.Wojtys, M.I.Maksymiuk, W.Wielgus-Kutrowska, B.Winiewska-Szajewska, M.Pavkov-Keller, T.Bertosa, B.Stefanic, Z.Luic, M.Bzowska, A.Lescic Asler, I.

(2023) Int J Biol Macromol 226: 37-50

  • DOI: https://doi.org/10.1016/j.ijbiomac.2022.12.001
  • Primary Citation of Related Structures:  
    7PVO

  • PubMed Abstract: 

    Purine nucleotide synthesis is realised only through the salvage pathway in pathogenic bacterium Helicobacter pylori. Therefore, the enzymes of this pathway, among them also the adenylosuccinate synthetase (AdSS), present potential new drug targets. This paper describes characterization of His 6 -tagged AdSS from H. pylori. Thorough analysis of 3D-structures of fully ligated AdSS (in a complex with guanosine diphosphate, 6-phosphoryl-inosine monophosphate, hadacidin and Mg 2+ ) and AdSS in a complex with inosine monophosphate (IMP) only, enabled identification of active site interactions crucial for ligand binding and enzyme activity. Combination of experimental and molecular dynamics (MD) simulations data, particularly emphasized the importance of hydrogen bond Arg135-IMP for enzyme dimerization and active site formation. The synergistic effect of substrates (IMP and guanosine triphosphate) binding was suggested by MD simulations. Several flexible elements of the structure (loops) are stabilized by the presence of IMP alone, however loops comprising residues 287-293 and 40-44 occupy different positions in two solved H. pylori AdSS structures. MD simulations discovered the hydrogen bond network that stabilizes the closed conformation of the residues 40-50 loop, only in the presence of IMP. Presented findings provide a solid basis for the design of new AdSS inhibitors as potential drugs against H. pylori.


  • Organizational Affiliation

    Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenylosuccinate synthetase411Helicobacter pylori 26695Mutation(s): 0 
Gene Names: purAHP_0255
EC: 6.3.4.4
UniProt
Find proteins for P56137 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56137 
Go to UniProtKB:  P56137
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56137
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.105α = 90
b = 61.326β = 98.417
c = 119.636γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2015/18/M/NZ1/00776
Ministry of Science and Higher Education (Poland)PolandBST-173300/BF

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description