5N9X

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.396 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


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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: 10.1111/febs.14163
  • Primary Citation of Related Structures:  

  • 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 wi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenylation domain
A, B
529Streptomyces spMutation(s): 0 
Gene Names: thr1
Find proteins for H6SG27 (Streptomyces sp)
Go to UniProtKB:  H6SG27
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
8QN
Query on 8QN

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B
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S},3~{R})-2-azanyl-3-oxidanyl-butanoate
C14 H21 N6 O9 P
YYBNSQASHCKPHX-DWVDDHQFSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
THR
Query on THR

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Download CCD File 
A
THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-GBXIJSLDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.396 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 179.022α = 90.00
b = 52.524β = 105.95
c = 110.119γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Database references