6ULW

Adenylation, ketoreductase, and pseudo Asub multidomain structure of a keto acid-selecting NRPS module

• PDB DOI: https://doi.org/10.2210/pdb6ULW/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Bacillus stratosphericus LAMA 585
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-08 Released: 2020-02-19 
• Deposition Author(s): Alonzo, D.A., Wang, J., Chiche-Lapierre, C., 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: 3.40 Å
• R-Value Free: 0.275 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 

Starting Models: 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: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration, native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration, native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 596.07 kDa 
• Atom Count: 37,840 
• Modelled Residue Count: 4,798 
• Deposited Residue Count: 5,308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid adenylation domain-containing protein	A, B, C, D	1,327	Bacillus stratosphericus LAMA 585	Mutation(s): 0  Gene Names: C883_1060

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], L [auth D], M [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.275 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.66	α = 90
b = 143.66	β = 90
c = 431.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Currently 6ULW does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Alonzo, D.A., Wang, J., Chiche-Lapierre, C., 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, Derived calculations, Refinement description