6NTE

Crystal Structure of Synechocystis Dihydroxyacid Dehydratase (DHAD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

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This is version 1.2 of the entry. See complete history


Literature

Cyanobacterial Dihydroxyacid Dehydratases Are a Promising Growth Inhibition Target.

Zhang, P.MacTavish, B.S.Yang, G.Chen, M.Roh, J.Newsome, K.R.Bruner, S.D.Ding, Y.

(2020) ACS Chem Biol 15: 2281-2288

  • DOI: https://doi.org/10.1021/acschembio.0c00507
  • Primary Citation of Related Structures:  
    6NTE

  • PubMed Abstract: 

    Microbes are essential to the global ecosystem, but undesirable microbial growth causes issues ranging from food spoilage and infectious diseases to harmful cyanobacterial blooms. The use of chemicals to control microbial growth has achieved significant success, while specific roles for a majority of essential genes in growth control remain unexplored. Here, we show the growth inhibition of cyanobacterial species by targeting an essential enzyme for the biosynthesis of branched-chain amino acids. Specifically, we report the biochemical, genetic, and structural characterization of dihydroxyacid dehydratase from the model cyanobacterium Synechocystis sp. PCC 6803 (SnDHAD). Our studies suggest that SnDHAD is an oxygen-stable enzyme containing a [2Fe-2S] cluster. Furthermore, we demonstrate that SnDHAD is selectively inhibited in vitro and in vivo by the natural product aspterric acid, which also inhibits the growth of representative bloom-forming Microcystis and Anabaena strains but has minimal effects on microbial pathogens with [4Fe-4S] containing DHADs. This study suggests DHADs as a promising target for the precise growth control of microbes and highlights the exploration of other untargeted essential genes for microbial management.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida 32610, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroxy-acid dehydratase
A, B
561Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: ilvDslr0452
EC: 4.2.1.9
UniProt
Find proteins for P74689 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore P74689 
Go to UniProtKB:  P74689
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP74689
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.79α = 90
b = 74.258β = 90.148
c = 80.68γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references, Structure summary
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description