5MG5 | pdb_00005mg5

A multi-component acyltransferase PhlABC from Pseudomonas protegens soaked with the monoacetylphloroglucinol (MAPG)

• PDB DOI: https://doi.org/10.2210/pdb5MG5/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudomonas protegens, Pseudomonas protegens Pf-5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-20 Released: 2017-12-20 
• Deposition Author(s): Pavkov-Keller, T., Schmidt, N.G., Kroutil, W., Gruber, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.44 Å
• R-Value Free: 
  0.221 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Structure and Catalytic Mechanism of a Bacterial Friedel-Crafts Acylase.

Pavkov-Keller, T., Schmidt, N.G., Zadlo-Dobrowolska, A., Kroutil, W., Gruber, K.

(2019) Chembiochem 20: 88-95

• PubMed: 30318713 
• DOI: https://doi.org/10.1002/cbic.201800462
• Primary Citation Related Structures: 
  5M3K, 5MG5


• PubMed Abstract: 
  

  C-C bond-forming reactions are key transformations for setting up the carbon frameworks of organic compounds. In this context, Friedel-Crafts acylation is commonly used for the synthesis of aryl ketones, which are common motifs in many fine chemicals and natural products. A bacterial multicomponent acyltransferase from Pseudomonas protegens (PpATase) catalyzes such Friedel-Crafts C-acylation of phenolic substrates in aqueous solution, reaching up to >99 % conversion without the need for CoA-activated reagents. We determined X-ray crystal structures of the native and ligand-bound complexes. This multimeric enzyme consists of three subunits: PhlA, PhlB, and PhlC, arranged in a Phl(A ₂ C ₂ ) ₂ B ₄ composition. The structure of a reaction intermediate obtained from crystals soaked with the natural substrate 1-(2,4,6-trihydroxyphenyl)ethanone together with site-directed mutagenesis studies revealed that only residues from the PhlC subunits are involved in the acyl transfer reaction, with Cys88 very likely playing a significant role during catalysis. These structural and mechanistic insights form the basis of further enzyme engineering efforts directed towards enhancing the substrate scope of this enzyme.

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Organizational Affiliation: 
• Austrian Centre of Industrial Biotechnology (ACIB), Petersgasse 14, 8010, Graz, Austria.
Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria.
Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28/2, 8010, Graz, Austria.
BioTechMed-Graz, Mozartgasse 12/II, 8010, Graz, Austria.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A4B4C4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A4B4C4 

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

Macromolecule Content 

• Total Structure Weight: 783.54 kDa 
• Atom Count: 54,522 
• Modeled Residue Count: 7,194 
• Deposited Residue Count: 7,248 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxymethylglutaryl-CoA synthase	A, D, G, J, M, P, S, V	362	Pseudomonas protegens	Mutation(s): 0  Gene Names: CEP86_09500

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2,4-diacetylphloroglucinol biosynthesis protein	B, E, H, K, N, Q, T, W	146	Pseudomonas protegens	Mutation(s): 0  Gene Names: CEP86_09490

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
2,4-diacetylphloroglucinol biosynthesis protein PhlC	C, F, I, L, O, R, U, X	398	Pseudomonas protegens Pf-5	Mutation(s): 0  Gene Names: phlC, PFL_5955
UniProt
Find proteins for Q4K420 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4K420  Go to UniProtKB:  Q4K420

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
13X	DA [auth L], FA [auth O], HA [auth R], Z [auth C]	benzene-1,3,5-triol C6 H6 O3 QCDYQQDYXPDABM-UHFFFAOYSA-N
ZN	AA [auth E], BA [auth H], CA [auth K], EA [auth N], GA [auth Q], IA [auth T], JA [auth W], Y [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SCY	C, F, I, L, O, R, U, X	L-PEPTIDE LINKING	C5 H9 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.44 Å
• R-Value Free:  0.221 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.793	α = 90
b = 229.775	β = 90
c = 311.129	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Pavkov-Keller, T., Schmidt, N.G., Kroutil, W., Gruber, K.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2018-10-31
  Changes: Data collection, Database references
• Version 1.2: 2019-02-27
  Changes: Data collection, Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary