5MG5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.44 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/10.1002/cbic.201800462
  • Primary Citation of 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.


  • Organizational Affiliation

    Austrian Centre of Industrial Biotechnology (ACIB), Petersgasse 14, 8010, Graz, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxymethylglutaryl-CoA synthase
A, D, G, J, M
A, D, G, J, M, P, S, V
362Pseudomonas protegensMutation(s): 0 
Gene Names: CEP86_09500
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
2,4-diacetylphloroglucinol biosynthesis protein
B, E, H, K, N
B, E, H, K, N, Q, T, W
146Pseudomonas protegensMutation(s): 0 
Gene Names: CEP86_09490
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
2,4-diacetylphloroglucinol biosynthesis protein PhlC
C, F, I, L, O
C, F, I, L, O, R, U, X
398Pseudomonas protegens Pf-5Mutation(s): 0 
Gene Names: phlCPFL_5955
UniProt
Find proteins for Q4K420 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5))
Explore Q4K420 
Go to UniProtKB:  Q4K420
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4K420
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
13X
Query on 13X

Download Ideal Coordinates CCD File 
DA [auth L],
FA [auth O],
HA [auth R],
Z [auth C]
benzene-1,3,5-triol
C6 H6 O3
QCDYQQDYXPDABM-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth H]
CA [auth K]
EA [auth N]
GA [auth Q]
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
IDChains TypeFormula2D DiagramParent
SCY
Query on SCY
C, F, I, L, O
C, F, I, L, O, R, U, X
L-PEPTIDE LINKINGC5 H9 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.44 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.793α = 90
b = 229.775β = 90
c = 311.129γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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