6ULW | pdb_00006ulw

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 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

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 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.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montreal, Quebec, Canada. [e-mail].

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 
• Modeled 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 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

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

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