6ULZ

Adenylation domain of the initiation module of LgrA mutant P483M

• PDB DOI: https://doi.org/10.2210/pdb6ULZ/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Brevibacillus parabrevis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-10-08 Released: 2020-02-19 
• Deposition Author(s): Chiche-Lapierre, C., Alonzo, D.A., Schmeing, T.M.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.246 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Starting Model: experimental

Literature

Structural basis of keto acid utilization in nonribosomal depsipeptide synthesis.

Alonzo, D.A., Chiche-Lapierre, C., Tarry, M.J., Wang, J., Schmeing, T.M.

(2020) Nat Chem Biol 16: 493-496

• PubMed: 32066969 
• DOI: https://doi.org/10.1038/s41589-020-0481-5
• Primary Citation of Related Structures:  
  6ULW, 6ULX, 6ULY, 6ULZ


• PubMed Abstract: 
  

  Nonribosomal depsipeptides are natural products composed of amino and hydroxy acid residues. The hydroxy acid residues often derive from α-keto acids, reduced by ketoreductase domains in the depsipeptide synthetases. Biochemistry and structures reveal the mechanism of discrimination for α-keto acids and a remarkable architecture: flanking intact adenylation and ketoreductase domains are sequences separated by >1,100 residues that form a split 'pseudoA _sub ' domain, structurally important for the depsipeptide module's synthetic cycle.

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Organizational Affiliation: 

Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montreal, Quebec, Canada.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 78.5 kDa 
• Atom Count: 4,723 
• Modelled Residue Count: 585 
• Deposited Residue Count: 687 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Linear gramicidin synthase subunit A	A	687	Brevibacillus parabrevis	Mutation(s): 1  Gene Names: lgrA
UniProt
Find proteins for Q70LM7 (Brevibacillus parabrevis) Explore Q70LM7  Go to UniProtKB:  Q70LM7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APC (Subject of Investigation/LOI)	E [auth A]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C11 H18 N5 O12 P3 CAWZRIXWFRFUQB-IOSLPCCCSA-N
KIV (Subject of Investigation/LOI)	F [auth A]	3-METHYL-2-OXOBUTANOIC ACID C5 H8 O3 QHKABHOOEWYVLI-UHFFFAOYSA-N
FMT	B [auth A], C [auth A], D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.246 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.18	α = 90
b = 161.18	β = 90
c = 138.63	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Chiche-Lapierre, C., Alonzo, D.A., Schmeing, T.M.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2020-03-04
  Changes: Database references
• Version 1.2: 2020-05-06
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description