3TEJ | pdb_00003tej

Crystal structure of a domain fragment involved in peptide natural product biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb3TEJ/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-15 Released: 2012-01-18 
• Deposition Author(s): Liu, Y., Zheng, T., Bruner, S.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Structural basis for phosphopantetheinyl carrier domain interactions in the terminal module of nonribosomal peptide synthetases.

Liu, Y., Zheng, T., Bruner, S.D.

(2011) Chem Biol 18: 1482-1488

• PubMed: 22118682 
• DOI: https://doi.org/10.1016/j.chembiol.2011.09.018
• Primary Citation Related Structures: 
  3TEJ


• PubMed Abstract: 
  

  Phosphopantetheine-modified carrier domains play a central role in the template-directed, biosynthesis of several classes of primary and secondary metabolites. Fatty acids, polyketides, and nonribosomal peptides are constructed on multidomain enzyme assemblies using phosphopantetheinyl thioester-linked carrier domains to traffic and activate building blocks. The carrier domain is a dynamic component of the process, shuttling pathway intermediates to sequential enzyme active sites. Here, we report an approach to structurally fix carrier domain/enzyme constructs suitable for X-ray crystallographic analysis. The structure of a two-domain construct of Escherichia coli EntF was determined with a conjugated phosphopantetheinyl-based inhibitor. The didomain structure is locked in an active orientation relevant to the chemistry of nonribosomal peptide biosynthesis. This structure provides details into the interaction of phosphopantetheine arm with the carrier domain and the active site of the thioesterase domain.

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Organizational Affiliation: 
• Department of Chemistry, Boston College, Chestnut Hill, MA 02167, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.27 kDa 
• Atom Count: 4,855 
• Modeled Residue Count: 606 
• Deposited Residue Count: 658 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enterobactin synthase component F	A, B	329	Escherichia coli K-12	Mutation(s): 0  Gene Names: entF, b0586, JW0578 EC: 2.7.7 (PDB Primary Data), 6.2.1.72 (UniProt), 6.3.2.14 (UniProt)
UniProt
Find proteins for P11454 (Escherichia coli (strain K12)) Explore P11454  Go to UniProtKB:  P11454

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UF0	A, B	L-PEPTIDE LINKING	C16 H31 N4 O11 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.4	α = 90
b = 90.36	β = 90
c = 97.53	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Liu, Y., Zheng, T., Bruner, S.D.

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary