6N8E | pdb_00006n8e

Crystal structure of holo-ObiF1, a five domain nonribosomal peptide synthetase from Burkholderia diffusa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.240 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

The structural basis of N-acyl-alpha-amino-beta-lactone formation catalyzed by a nonribosomal peptide synthetase.

Kreitler, D.F.Gemmell, E.M.Schaffer, J.E.Wencewicz, T.A.Gulick, A.M.

(2019) Nat Commun 10: 3432-3432

  • DOI: https://doi.org/10.1038/s41467-019-11383-7
  • Primary Citation Related Structures: 
    6N8E

  • PubMed Abstract: 

    Nonribosomal peptide synthetases produce diverse natural products using a multidomain architecture where the growing peptide, attached to an integrated carrier domain, is delivered to neighboring catalytic domains for bond formation and modification. Investigation of these systems can lead to the discovery of new structures, unusual biosynthetic transformations, and to the engineering of catalysts for generating new products. The antimicrobial β-lactone obafluorin is produced nonribosomally from dihydroxybenzoic acid and a β-hydroxy amino acid that cyclizes into the β-lactone during product release. Here we report the structure of the nonribosomal peptide synthetase ObiF1, highlighting the structure of the β-lactone-producing thioesterase domain and an interaction between the C-terminal MbtH-like domain with an upstream adenylation domain. Biochemical assays examine catalytic promiscuity, provide mechanistic insight, and demonstrate utility for generating obafluorin analogs. These results advance our understanding of the structural cycle of nonribosomal peptide synthetases and provide insights into the production of β-lactone natural products.


  • Organizational Affiliation
    • Department of Structural Biology, Jacobs School of Medicine & Biomedical Sciences at the University at Buffalo, 955 Main Street, Buffalo, NY, 14203, USA.

Macromolecule Content 

  • Total Structure Weight: 153.27 kDa 
  • Atom Count: 10,018 
  • Modeled Residue Count: 1,332 
  • Deposited Residue Count: 1,410 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
holo-ObiF11,410Burkholderia diffusaMutation(s): 0 
UniProt
Find proteins for A0A5H1ZR44 (Burkholderia diffusa)
Explore A0A5H1ZR44 
Go to UniProtKB:  A0A5H1ZR44
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5H1ZR44
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PNS
(Subject of Investigation/LOI)

Query on PNS



Download:Ideal Coordinates CCD File
B [auth A]4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
KFJ
(Subject of Investigation/LOI)

Query on KFJ



Download:Ideal Coordinates CCD File
D [auth A]4-(4-nitrophenyl)-L-threonine
C10 H12 N2 O5
HUGPLGZGZBFEOQ-BDAKNGLRSA-N
KFG

Query on KFG



Download:Ideal Coordinates CCD File
C [auth A]dimethyl hydrogen phosphate
C2 H7 O4 P
KKUKTXOBAWVSHC-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.240 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.325α = 90
b = 154.345β = 90
c = 183.905γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM116957

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description