5U89

Crystal structure of a cross-module fragment from the dimodular NRPS DhbF

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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Literature

X-Ray Crystallography and Electron Microscopy of Cross- and Multi-Module Nonribosomal Peptide Synthetase Proteins Reveal a Flexible Architecture.

Tarry, M.J., Haque, A.S., Bui, K.H., Schmeing, T.M.

(2017) Structure 25: 783-793.e4

  • DOI: 10.1016/j.str.2017.03.014
  • Primary Citation of Related Structures:  
    5U89

  • PubMed Abstract: 

    • Nonribosomal peptide synthetases (NRPS) are macromolecular machines that produce peptides with diverse activities. Structural information exists for domains, didomains, and even modules, but little is known about higher-order organization. We performed a multi-technique study on constructs from the dimodular NRPS DhbF ...

    Nonribosomal peptide synthetases (NRPS) are macromolecular machines that produce peptides with diverse activities. Structural information exists for domains, didomains, and even modules, but little is known about higher-order organization. We performed a multi-technique study on constructs from the dimodular NRPS DhbF. We determined a crystal structure of a cross-module construct including the adenylation (A) and peptidyl carrier protein (PCP) domains from module 1 and the condensation domain from module 2, complexed with an adenosine-vinylsulfonamide inhibitor and an MbtH-like protein (MLP). The action of the inhibitor and the role of the MLP were investigated using adenylation reactions and isothermal titration calorimetry. In the structure, the PCP and A domains adopt a novel conformation, and noncovalent, cross-module interactions are limited. We calculated envelopes of dimodular DhbF using negative-stain electron microscopy. The data show large conformational variability between modules. Together, our results suggest that NRPSs lack a uniform, rigid supermodular architecture.

    Organizational Affiliation: 

    Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada. Electronic address: martin.schmeing@mcgill.ca.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Amino acid adenylation domain proteinA1080Geobacillus sp. Y4.1MC1Mutation(s): 0 
Gene Names: GY4MC1_0171
UniProt
Find proteins for A0A7U3YCA6 (Geobacillus sp. (strain Y4.1MC1))
Explore A0A7U3YCA6 
Go to UniProtKB:  A0A7U3YCA6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7U3YCA6
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MbtH domain proteinB83Geobacillus sp. Y4.1MC1Mutation(s): 0 
Gene Names: GY4MC1_0172
UniProt
Find proteins for A0A7U3YBY3 (Geobacillus sp. (strain Y4.1MC1))
Explore A0A7U3YBY3 
Go to UniProtKB:  A0A7U3YBY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7U3YBY3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MJ8
Query on MJ8
Download Ideal Coordinates CCD File 
C [auth A]5'-({[(2R)-3-amino-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}propyl]sulfonyl}amino)-5'-deoxyadenosine
C24 H42 N9 O12 P S2
AKPDLNPLPXRYTO-XGVFZYDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.51α = 90
b = 119.51β = 90
c = 589.647γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaFDN-148472

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-05-17
    Changes: Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence