Crystal structure of Adenylosuccinate lyase from Thermus thermophilus HB8, TtPurB

Experimental Data Snapshot

  • Resolution: 2.38 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 

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Crystal structure of adenylosuccinate lyase from the thermophilic bacterium Thermus thermophilus HB8.

Nemoto, N.Kawai, G.Sampei, G.I.

(2023) Acta Crystallogr F Struct Biol Commun 79: 278-284

  • DOI: https://doi.org/10.1107/S2053230X23009020
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Adenylosuccinate lyase (PurB) catalyzes two distinct reactions in the purine nucleotide biosynthetic pathway using the same active site. The ability to recognize two different sets of substrates is of structural and evolutionary interest. In the present study, the crystal structure of PurB from the thermophilic bacterium Thermus thermophilus HB8 (TtPurB) was determined at a resolution of 2.38 Å by molecular replacement using a structure predicted by AlphaFold2 as a template. The asymmetric unit of the TtPurB crystal contained two TtPurB molecules, and some regions were disordered in the crystal structure. The disordered regions were the substrate-binding site and domain 3. TtPurB forms a homotetramer and the monomer is composed of three domains (domains 1, 2 and 3), which is a typical structure for the aspartase/fumarase superfamily. Molecular dynamics simulations with and without substrate/product were performed using a full-length model of TtPurB which was obtained before deletion of the disordered regions. The substrates and products were bound to the model structures during the MD simulations. The fluctuations of amino-acid residues were greater in the disordered regions and became smaller upon the binding of substrate or product. These results demonstrate that the full-length model obtained using AlphaFold2 can be used to generate the coordinates of disordered regions within the crystal structure.

  • Organizational Affiliation

    Faculty of Advanced Engineering, Chiba Institute of Technology, Narashino, Chiba 275-0016, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenylosuccinate lyase
A, B
457Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1513
Find proteins for Q5SI61 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SI61 
Go to UniProtKB:  Q5SI61
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SI61
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.38 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.657α = 90
b = 158.657β = 90
c = 151.634γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release