6MFW | pdb_00006mfw

Crystal structure of a 4-domain construct of LgrA in the substrate donation state

• PDB DOI: https://doi.org/10.2210/pdb6MFW/pdb

• Classification: LIGASE
• Organism(s): Brevibacillus parabrevis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-09-12 Released: 2019-11-20 
• Deposition Author(s): Reimer, J.M., Eivaskhani, M., Schmeing, T.M.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Other government

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility.

Reimer, J.M., Eivaskhani, M., Harb, I., Guarne, A., Weigt, M., Schmeing, T.M.

(2019) Science 366

• PubMed: 31699907 
• DOI: https://doi.org/10.1126/science.aaw4388
• Primary Citation Related Structures: 
  6MFW, 6MFX, 6MFY, 6MFZ, 6MG0


• PubMed Abstract: 
  

  Nonribosomal peptide synthetases (NRPSs) are biosynthetic enzymes that synthesize natural product therapeutics using a modular synthetic logic, whereby each module adds one aminoacyl substrate to the nascent peptide. We have determined five x-ray crystal structures of large constructs of the NRPS linear gramicidin synthetase, including a structure of a full core dimodule in conformations organized for the condensation reaction and intermodular peptidyl substrate delivery. The structures reveal differences in the relative positions of adjacent modules, which are not strictly coupled to the catalytic cycle and are consistent with small-angle x-ray scattering data. The structures and covariation analysis of homologs allowed us to create mutants that improve the yield of a peptide from a module-swapped dimodular NRPS.

---

Organizational Affiliation: 
• Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada.
Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005 Paris, France.
Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 139.74 kDa 
• Atom Count: 9,699 
• Modeled Residue Count: 1,181 
• Deposited Residue Count: 1,210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Linear gramicidin synthase subunit A	A	1,210	Brevibacillus parabrevis	Mutation(s): 0  Gene Names: lgrA
UniProt
Find proteins for Q70LM7 (Brevibacillus parabrevis) Explore Q70LM7  Go to UniProtKB:  Q70LM7

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APC	D [auth A]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C11 H18 N5 O12 P3 CAWZRIXWFRFUQB-IOSLPCCCSA-N
FON	C [auth A]	N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid C20 H23 N7 O7 VVIAGPKUTFNRDU-OLZOCXBDSA-N
JQG	B [auth A]	(2~{R})-~{N}-[3-[2-[[(2~{S})-2-formamido-3-methyl-butanoyl]amino]ethylamino]-3-oxidanylidene-propyl]-3,3-dimethyl-2-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-butanamide C17 H32 N4 O9 P SZJRFDKIBVCSLN-KBPBESRZSA-N
VAL	E [auth A]	VALINE C5 H11 N O2 KZSNJWFQEVHDMF-BYPYZUCNSA-N
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.37	α = 90
b = 133.87	β = 90
c = 162.099	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Reimer, J.M., Eivaskhani, M., Schmeing, T.M.

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	106615
Other government	Canada	--

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary