3RG2

Structure of a two-domain NRPS fusion protein containing the EntE adenylation domain and EntB aryl-carrier protein from enterobactin biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural and Functional Investigation of the Intermolecular Interaction between NRPS Adenylation and Carrier Protein Domains.

Sundlov, J.A.Shi, C.Wilson, D.J.Aldrich, C.C.Gulick, A.M.

(2012) Chem.Biol. 19: 188-198

  • DOI: 10.1016/j.chembiol.2011.11.013

  • PubMed Abstract: 
  • Nonribosomal peptide synthetases (NRPSs) are modular proteins that produce peptide antibiotics and siderophores. These enzymes act as catalytic assembly lines where substrates, covalently bound to integrated carrier domains, are delivered to adjacent ...

    Nonribosomal peptide synthetases (NRPSs) are modular proteins that produce peptide antibiotics and siderophores. These enzymes act as catalytic assembly lines where substrates, covalently bound to integrated carrier domains, are delivered to adjacent catalytic domains. The carrier domains are initially loaded by adenylation domains, which use two distinct conformations to catalyze sequentially the adenylation of the substrate and the thioesterification of the pantetheine cofactor. We have used a mechanism-based inhibitor to determine the crystal structure of an engineered adenylation-carrier domain protein illustrating the intermolecular interaction between the adenylation and carrier domains. This structure enabled directed mutations to improve the interaction between nonnative partner proteins. Comparison with prior NRPS adenylation domain structures provides insights into the assembly line dynamics of these modular enzymes.


    Organizational Affiliation

    Hauptman-Woodward Institute and Department of Structural Biology, University at Buffalo, Buffalo, NY 14203 USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enterobactin synthase component E (entE), 2,3-dihydro-2,3-dihydroxybenzoate synthetase, isochroismatase (Entb)
A, B, C, D, E, F, G, H, I, J
617Escherichia 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
PNS
Query on PNS

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
SVS
Query on SVS

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
5'-deoxy-5'-({[2-(2-hydroxyphenyl)ethyl]sulfonyl}amino)adenosine
C18 H22 N6 O6 S
NIEGSPNRJDKALY-SCFUHWHPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SVSKd: 63000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 160.575α = 90.00
b = 101.771β = 107.06
c = 240.678γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
BALBESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-07
    Type: Initial release
  • Version 1.1: 2012-03-28
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Refinement description, Source and taxonomy
  • Version 1.3: 2019-07-17
    Type: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2019-08-14
    Type: Data collection