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- PDB-11km: SpACSA with propyl-AMP and CoA -

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Basic information

Entry
Database: PDB / ID: 11km
TitleSpACSA with propyl-AMP and CoA
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / acetyl-CoA synthetase / complex
Function / homology
Function and homology information


Ethanol oxidation / acetate-CoA ligase / acetyl-CoA synthetase activity / acetyl-CoA biosynthetic process / AMP binding / mitochondrial matrix / nucleus / cytosol / cytoplasm
Similarity search - Function
Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / 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
COENZYME A / ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / Probable acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsLi, M. / Zhou, M. / Marmorstein, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Structure / Year: 2026
Title: Ligand-dependent interdomain rearrangements drive catalysis by acetyl-CoA synthetases.
Authors: Meng Li / Mingyang Zhou / Ronen Marmorstein /
Abstract: Acetyl-coenzyme A synthetases convert ATP, acetate, and coenzyme A (CoA) into acetyl-CoA, a central metabolite that fuels lipid biosynthesis and regulates protein and RNA acetylation. ACS enzymes ...Acetyl-coenzyme A synthetases convert ATP, acetate, and coenzyme A (CoA) into acetyl-CoA, a central metabolite that fuels lipid biosynthesis and regulates protein and RNA acetylation. ACS enzymes contain N- and C-terminal domains that coordinate a two-step ping-pong mechanism involving sequential adenylation and thioester formation at the interdomain interface. How domain motions coordinate these chemical steps remains unclear. Here, we report single-particle cryo-electron microscopy structures of Schizosaccharomyces pombe ACSA captured in apo, pre-adenylation, intermediate, and product states. These structures reveal ligand-dependent reorganization of the C-terminal domain: apo and pre-adenylation forms display increased conformational heterogeneity, whereas intermediate- and product-bound states adopt ordered conformations compatible with catalysis. Structure-guided mutagenesis and in vitro activity assays, together with sequence conservation, support the functional importance and evolutionary conservation of the observed conformational transitions across ACS homologs. These findings establish a ligand-coupled interdomain rearrangement mechanism underlying catalysis by ACS enzymes and a structural framework for inhibitor development.
History
DepositionMar 2, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1243
Polymers74,9671
Non-polymers1,1572
Water00
1
A: Acetyl-coenzyme A synthetase
hetero molecules

A: Acetyl-coenzyme A synthetase
hetero molecules

A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,3719
Polymers224,9003
Non-polymers3,4716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))

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Components

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


Mass: 74966.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPCC191.02c, SPCC417.14c / Production host: Escherichia coli (E. coli) / References: UniProt: P78773, acetate-CoA ligase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PRX / ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / ADENOSINE-5'-PROPYLPHOSPHATE


Mass: 389.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N5O7P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: SpACSA with CoA and propyl-AMP / Type: COMPLEX
Details: Propyl-AMP is non-hydrolysable analog of acetyl-AMP. Cryo-EM density was observed for CoA, but only the portion with well-defined density was included in the final model.
Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Buffer solutionpH: 7.5
SpecimenEmbedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 46.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132946 / Symmetry type: POINT
RefinementHighest resolution: 2.97 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0055218
ELECTRON MICROSCOPYf_angle_d0.567115
ELECTRON MICROSCOPYf_dihedral_angle_d6.879772
ELECTRON MICROSCOPYf_chiral_restr0.048791
ELECTRON MICROSCOPYf_plane_restr0.004902

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