5JA1

EntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to the MbtH-Like Protein YbdZ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of a Nonribosomal Peptide Synthetase Module Bound to MbtH-like Proteins Support a Highly Dynamic Domain Architecture.

Miller, B.R.Drake, E.J.Shi, C.Aldrich, C.C.Gulick, A.M.

(2016) J.Biol.Chem. 291: 22559-22571

  • DOI: 10.1074/jbc.M116.746297
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nonribosomal peptide synthetases (NRPSs) produce a wide variety of peptide natural products. During synthesis, the multidomain NRPSs act as an assembly line, passing the growing product from one module to the next. Each module generally consists of a ...

    Nonribosomal peptide synthetases (NRPSs) produce a wide variety of peptide natural products. During synthesis, the multidomain NRPSs act as an assembly line, passing the growing product from one module to the next. Each module generally consists of an integrated peptidyl carrier protein, an amino acid-loading adenylation domain, and a condensation domain that catalyzes peptide bond formation. Some adenylation domains interact with small partner proteins called MbtH-like proteins (MLPs) that enhance solubility or activity. A structure of an MLP bound to an adenylation domain has been previously reported using a truncated adenylation domain, precluding any insight that might be derived from understanding the influence of the MLP on the intact adenylation domain or on the dynamics of the entire NRPS module. Here, we present the structures of the full-length NRPS EntF bound to the MLPs from Escherichia coli and Pseudomonas aeruginosa These new structures, along with biochemical and bioinformatics support, further elaborate the residues that define the MLP-adenylation domain interface. Additionally, the structures highlight the dynamic behavior of NRPS modules, including the module core formed by the adenylation and condensation domains as well as the orientation of the mobile thioesterase domain.


    Related Citations: 
    • Structures of two distinct conformations of holo-non-ribosomal peptide synthetases.
      Drake, E.J.,Miller, B.R.,Shi, C.,Tarrasch, J.T.,Sundlov, J.A.,Allen, C.L.,Skiniotis, G.,Aldrich, C.C.,Gulick, A.M.
      (2016) Nature 529: 235


    Organizational Affiliation

    From the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enterobactin synthase component F
A
1295Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: entF
EC: 2.7.7.-
Find proteins for P11454 (Escherichia coli (strain K12))
Go to UniProtKB:  P11454
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Enterobactin biosynthesis protein YbdZ
B
74Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ybdZ
Find proteins for P18393 (Escherichia coli (strain K12))
Go to UniProtKB:  P18393
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
75C
Query on 75C

Download SDF File 
Download CCD File 
A
5'-({[(2R,3S)-3-amino-4-hydroxy-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}butyl]sulfonyl}amino)-5'-deoxyadenosine
C25 H44 N9 O13 P S2
ISNNGRBZFMWGAL-DROAMXOMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.185 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 161.185α = 90.00
b = 57.679β = 97.93
c = 183.945γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM116957

Revision History 

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations