6SL8

Diaminobutyrate acetyltransferase EctA from Paenibacillus lautus in complex with its substrate L-2,4-diaminobutyric acid (DAB)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

The architecture of the diaminobutyrate acetyltransferase active site provides mechanistic insight into the biosynthesis of the chemical chaperone ectoine.

Richter, A.A.Kobus, S.Czech, L.Hoeppner, A.Zarzycki, J.Erb, T.J.Lauterbach, L.Dickschat, J.S.Bremer, E.Smits, S.H.J.

(2020) J Biol Chem 295: 2822-2838

  • DOI: https://doi.org/10.1074/jbc.RA119.011277
  • Primary Citation of Related Structures:  
    6SJY, 6SK1, 6SL8, 6SLK, 6SLL

  • PubMed Abstract: 

    Ectoine is a solute compatible with the physiologies of both prokaryotic and eukaryotic cells and is widely synthesized by bacteria as an osmotic stress protectant. Because it preserves functional attributes of proteins and macromolecular complexes, it is considered a chemical chaperone and has found numerous practical applications. However, the mechanism of its biosynthesis is incompletely understood. The second step in ectoine biosynthesis is catalyzed by l-2,4-diaminobutyrate acetyltransferase (EctA; EC 2.3.1.178), which transfers the acetyl group from acetyl-CoA to EctB-formed l-2,4-diaminobutyrate (DAB), yielding N -γ-acetyl-l-2,4-diaminobutyrate ( N -γ-ADABA), the substrate of ectoine synthase (EctC). Here, we report the biochemical and structural characterization of the EctA enzyme from the thermotolerant bacterium Paenibacillus lautus ( Pl ). We found that ( Pl )EctA forms a homodimer whose enzyme activity is highly regiospecific by producing N -γ-ADABA but not the ectoine catabolic intermediate N -α-acetyl-l-2,4-diaminobutyric acid. High-resolution crystal structures of ( Pl )EctA (at 1.2-2.2 Å resolution) (i) for its apo-form, (ii) in complex with CoA, (iii) in complex with DAB, (iv) in complex with both CoA and DAB, and (v) in the presence of the product N -γ-ADABA were obtained. To pinpoint residues involved in DAB binding, we probed the structure-function relationship of ( Pl )EctA by site-directed mutagenesis. Phylogenomics shows that EctA-type proteins from both Bacteria and Archaea are evolutionarily highly conserved, including catalytically important residues. Collectively, our biochemical and structural findings yielded detailed insights into the catalytic core of the EctA enzyme that laid the foundation for unraveling its reaction mechanism.


  • Organizational Affiliation

    Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-2,4-diaminobutyric acid acetyltransferase186Paenibacillus sp. Y412MC10Mutation(s): 0 
Gene Names: ectAGYMC10_5665
EC: 2.3.1.178
UniProt
Find proteins for D3EKC1 (Geobacillus sp. (strain Y412MC10))
Explore D3EKC1 
Go to UniProtKB:  D3EKC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3EKC1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.979α = 90
b = 57.979β = 90
c = 134.461γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 1.2: 2020-03-11
    Changes: Database references
  • Version 2.0: 2021-06-30
    Changes: Advisory, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description