5JA2 | pdb_00005ja2

EntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to the non-Native MbtH-Like Protein PA2412

• PDB DOI: https://doi.org/10.2210/pdb5JA2/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli K-12, Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-11 Released: 2016-09-14 
• Deposition Author(s): Miller, B.R., Gulick, A.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

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 Biological Chem 291: 22559-22571

• PubMed: 27597544 
• DOI: https://doi.org/10.1074/jbc.M116.746297
• Primary Citation Related Structures: 
  5JA1, 5JA2


• 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 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.

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Organizational Affiliation: 
• From the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203.
the Department of Structural Biology, University at Buffalo, Buffalo, New York 14203, and.
the Center for Drug Design and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455.
From the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 151.92 kDa 
• Atom Count: 9,900 
• Modeled Residue Count: 1,306 
• Deposited Residue Count: 1,369 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enterobactin synthase component F	A	1,295	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MbtH-Like Protein PA2412	B	74	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA2412
UniProt
Find proteins for Q9I169 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I169  Go to UniProtKB:  Q9I169

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
75C	C [auth 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
BU9	D [auth A], E [auth A]	Meso-2,3-Butanediol C4 H10 O2 OWBTYPJTUOEWEK-ZXZARUISSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.27	α = 90
b = 57.69	β = 97.62
c = 182.424	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Miller, B.R., Gulick, A.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM116957

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2016-11-16
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary