7MMZ

Crystal Structure of Acetyl-coenzyme A synthetase from Legionella pneumophila Philadelphia 1 in complex with ethyl-AMP

• PDB DOI: https://doi.org/10.2210/pdb7MMZ/pdb

• Classification: LIGASE
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-04-30 Released: 2021-05-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.225 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Bacterial structural genomics target enabled by a recently discovered potent fungal acetyl-CoA synthetase inhibitor.

DeBouver, N.D., Bolejack, M.J., Esan, T.E., Krysan, D.J., Hagen, T.J., Abendroth, J.

(2023) Acta Crystallogr F Struct Biol Commun 

• PubMed: 37223974 
• DOI: https://doi.org/10.1107/S2053230X23003801
• Primary Citation of Related Structures:  
  7MMZ


• PubMed Abstract: 
  

  The compound ethyl-adenosyl monophosphate ester (ethyl-AMP) has been shown to effectively inhibit acetyl-CoA synthetase (ACS) enzymes and to facilitate the crystallization of fungal ACS enzymes in various contexts. In this study, the addition of ethyl-AMP to a bacterial ACS from Legionella pneumophila resulted in the determination of a co-crystal structure of this previously elusive structural genomics target. The dual functionality of ethyl-AMP in both inhibiting ACS enzymes and promoting crystallization establishes its significance as a valuable resource for advancing structural investigations of this class of proteins.

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Organizational Affiliation: 

UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98102, USA.

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: 71.07 kDa 
• Atom Count: 4,376 
• Modelled Residue Count: 559 
• Deposited Residue Count: 635 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-coenzyme A synthetase	A	635	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: acsB, lpg0127 EC: 6.2.1.1
UniProt
Find proteins for Q5ZZ84 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZZ84  Go to UniProtKB:  Q5ZZ84

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WTA (Subject of Investigation/LOI)	B [auth A]	5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine C12 H18 N5 O7 P MXYRBUKSSSUFQO-WOUKDFQISA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.225 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/m37mmz

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.93	α = 90
b = 74.93	β = 90
c = 228.79	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2021-05-26
  Type: Initial release
  
• Version 1.1: 2023-06-07
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description