4IZ6

Structure of EntE and EntB, an NRPS adenylation-PCP fusion protein with pseudo translational symmetry


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure determination of the functional domain interaction of a chimeric nonribosomal peptide synthetase from a challenging crystal with noncrystallographic translational symmetry.

Sundlov, J.A.Gulick, A.M.

(2013) Acta Crystallogr.,Sect.D 69: 1482-1492

  • DOI: 10.1107/S0907444913009372

  • PubMed Abstract: 
  • The nonribosomal peptide synthetases (NRPSs) are a family of modular proteins that contain multiple catalytic domains joined in a single protein. Together, these domains work to produce chemically diverse peptides, including compounds with antibiotic ...

    The nonribosomal peptide synthetases (NRPSs) are a family of modular proteins that contain multiple catalytic domains joined in a single protein. Together, these domains work to produce chemically diverse peptides, including compounds with antibiotic activity or that play a role in iron acquisition. Understanding the structural mechanisms that govern the domain interactions has been a long-standing goal. During NRPS synthesis, amino-acid substrates are loaded onto integrated carrier protein domains through the activity of NRPS adenylation domains. The structures of two adenylation domain-carrier protein domain complexes have recently been determined in an effort that required the use of a mechanism-based inhibitor to trap the domain interaction. Here, the continued analysis of these proteins is presented, including a higher resolution structure of an engineered di-domain protein containing the EntE adenylation domain fused with the carrier protein domain of its partner EntB. The protein crystallized in a novel space group in which molecular replacement and refinement were challenged by noncrystallographic pseudo-translational symmetry. The structure determination and how the molecular packing impacted the diffraction intensities are reported. Importantly, the structure illustrates that in this new crystal form the functional interface between the adenylation domain and the carrier protein domain remains the same as that observed previously. At a resolution that allows inclusion of water molecules, additional interactions are observed between the two protein domains and between the protein and its ligands. In particular, a highly solvated region that surrounds the carrier protein cofactor is described.


    Organizational Affiliation

    Hauptman-Woodward Medical Research Institute and Department of Structural Biology, University at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enterobactin synthase component E, Isochorismatase
A, B
635Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: entE, entB (entG)
EC: 6.3.2.14 6.3.2.14
Find proteins for P10378 (Escherichia coli (strain K12))
Go to UniProtKB:  P10378
Find proteins for P0ADI4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADI4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNS
Query on PNS

Download SDF File 
Download CCD File 
A, B
4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
1HZ
Query on 1HZ

Download SDF File 
Download CCD File 
A, B
5'-deoxy-5'-({[2-(2,3-dihydroxyphenyl)ethyl]sulfonyl}amino)adenosine
C18 H22 N6 O7 S
JESVQFVPCGDKBX-XKLVTHTNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.250 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.990α = 90.00
b = 119.110β = 90.00
c = 99.770γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-10-09
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Refinement description, Source and taxonomy