5N9W

Structure of adenylation domain THR1 involved in the biosynthesis of 4-chlorothreonine in Streptomyces SP.OH-5093, apo structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the adenylation domain Thr1 involved in the biosynthesis of 4-chlorothreonine in Streptomyces sp. OH-5093-protein flexibility and molecular bases of substrate specificity.

Scaglione, A.Fullone, M.R.Montemiglio, L.C.Parisi, G.Zamparelli, C.Vallone, B.Savino, C.Grgurina, I.

(2017) FEBS J 284: 2981-2999

  • DOI: https://doi.org/10.1111/febs.14163
  • Primary Citation of Related Structures:  
    5N9W, 5N9X

  • PubMed Abstract: 

    We determined the crystal structure of Thr1, the self-standing adenylation domain involved in the nonribosomal-like biosynthesis of free 4-chlorothreonine in Streptomyces sp. OH-5093. Thr1 shows two monomers in the crystallographic asymmetric unit with different relative orientations of the C- and N-terminal subdomains both in the presence of substrates and in the unliganded form. Cocrystallization with substrates, adenosine 5'-triphosphate and l-threonine, yielded one monomer containing the two substrates and the other in complex with l-threonine adenylate, locked in a postadenylation state. Steady-state kinetics showed that Thr1 activates l-Thr and its stereoisomers, as well as d-Ala, l- and d-Ser, albeit with lower efficiency. Modeling of these substrates in the active site highlighted the molecular bases of substrate discrimination. This work provides the first crystal structure of a threonine-activating adenylation enzyme, a contribution to the studies on conformational rearrangement in adenylation domains and on substrate recognition in nonribosomal biosynthesis.


  • Organizational Affiliation

    Department of Biochemical Sciences "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenylation domain
A, B
529Streptomyces sp.Mutation(s): 0 
Gene Names: thr1
UniProt
Find proteins for H6SG27 (Streptomyces sp)
Explore H6SG27 
Go to UniProtKB:  H6SG27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6SG27
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.633α = 90
b = 52.806β = 105.81
c = 108.861γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sapienza University of RomeItalyC26A14P4BP
Regione Lazio ProToxItalyFILAS-RU-2014-1020

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description