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- PDB-9g79: Cryo-EM structure of Acetyl-coenzyme A synthetase (AcsA) dimer -

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Basic information

Entry
Database: PDB / ID: 9g79
TitleCryo-EM structure of Acetyl-coenzyme A synthetase (AcsA) dimer
ComponentsAcetyl-coenzyme A synthetase
KeywordsBIOSYNTHETIC PROTEIN / Ac-CoA synthetase AcsA / acetate switch / GCN5-related N-acetyltransferase AcuA
Function / homology
Function and homology information


acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process / membrane raft / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsZheng, L.J. / Du, Y. / Bange, G.
Funding support Germany, United Kingdom, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)324652314 Germany
Leverhulme TrustECF-2022-525 United Kingdom
Wellcome TrustWT096570 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105184332 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Regulation of acetyl-CoA biosynthesis via an intertwined acetyl-CoA synthetase/acetyltransferase complex.
Authors: Liujuan Zheng / Yifei Du / Wieland Steinchen / Mathias Girbig / Frank Abendroth / Ekaterina Jalomo-Khayrova / Patricia Bedrunka / Isabelle Bekeredjian-Ding / Christopher-Nils Mais / Georg K ...Authors: Liujuan Zheng / Yifei Du / Wieland Steinchen / Mathias Girbig / Frank Abendroth / Ekaterina Jalomo-Khayrova / Patricia Bedrunka / Isabelle Bekeredjian-Ding / Christopher-Nils Mais / Georg K A Hochberg / Johannes Freitag / Gert Bange /
Abstract: Acetyl-CoA synthetase (Acs) generates acetyl-coenzyme A (Ac-CoA) but its excessive activity can deplete ATP and lead to a growth arrest. To prevent this, Acs is regulated through Ac-CoA-dependent ...Acetyl-CoA synthetase (Acs) generates acetyl-coenzyme A (Ac-CoA) but its excessive activity can deplete ATP and lead to a growth arrest. To prevent this, Acs is regulated through Ac-CoA-dependent feedback inhibition executed by Ac-CoA-dependent acetyltransferases such as AcuA in Bacillus subtilis. AcuA acetylates the catalytic lysine of AcsA turning the synthetase inactive. Here, we report that AcuA and AcsA form a tightly intertwined complex - the C-terminal domain binds to acetyltransferase domain of AcuA, while the C-terminus of AcuA occupies the CoA-binding site in the N-terminal domain of AcsA. Formation of the complex reduces AcsA activity in addition to the well-established acetylation of the catalytic lysine 549 in AcsA which we show can disrupt the complex. Thus, different modes of regulation accomplished through AcuA adjust AcsA activity to the concentrations of the different substrates of the reaction. In summary, our study provides detailed mechanistic insights into the regulatory framework underlying acetyl-CoA biosynthesis from acetate.
History
DepositionJul 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Acetyl-coenzyme A synthetase
A: Acetyl-coenzyme A synthetase


Theoretical massNumber of molelcules
Total (without water)129,9522
Polymers129,9522
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Acetyl-coenzyme A synthetase / AcCoA synthetase / Acs / Acetate--CoA ligase / Acyl-activating enzyme


Mass: 64975.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: acsA, BSU29680 / Production host: Escherichia coli (E. coli) / References: UniProt: P39062, acetate-CoA ligase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dimer of AcsA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Bacillus subtilis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: dev_4620: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 169773 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037450
ELECTRON MICROSCOPYf_angle_d0.52710106
ELECTRON MICROSCOPYf_dihedral_angle_d4.387978
ELECTRON MICROSCOPYf_chiral_restr0.0431024
ELECTRON MICROSCOPYf_plane_restr0.0071304

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