4IZ6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 

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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 D Biol Crystallogr 69: 1482-1492

  • DOI: 10.1107/S0907444913009372
  • Primary Citation of Related Structures:  
    4IZ6

  • 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 activity or that play a role in iron acquisition ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Enterobactin synthase component E, IsochorismataseA, B635Escherichia coliMutation(s): 0 
Gene Names: b0594entEentE and entBJW0586b0595entBentGJW0587
EC: 2.7.7.58 (PDB Primary Data), 2.3.1 (PDB Primary Data), 6.3.2.14 (UniProt), 2.5.1 (UniProt), 3.3.2.1 (UniProt)
UniProt
Find proteins for P0ADI4 (Escherichia coli (strain K12))
Explore P0ADI4 
Go to UniProtKB:  P0ADI4
Find proteins for P10378 (Escherichia coli (strain K12))
Explore P10378 
Go to UniProtKB:  P10378
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1HZ (Subject of Investigation/LOI)
Query on 1HZ

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]5'-deoxy-5'-({[2-(2,3-dihydroxyphenyl)ethyl]sulfonyl}amino)adenosine
C18 H22 N6 O7 S
JESVQFVPCGDKBX-XKLVTHTNSA-N
 Ligand Interaction
PNS (Subject of Investigation/LOI)
Query on PNS

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.99α = 90
b = 119.11β = 90
c = 99.77γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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