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- EMDB-51121: Cryo-EM structure of Acetyl-coenzyme A synthetase (AcsA) dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-51121
TitleCryo-EM structure of Acetyl-coenzyme A synthetase (AcsA) dimer
Map dataOverall map
Sample
  • Complex: AcsA-AcuA complex
    • Protein or peptide: Acetyl-coenzyme A synthetase
    • Protein or peptide: Acetoin utilization protein AcuA
KeywordsAc-CoA synthetase AcsA / acetate switch / GCN5-related N-acetyltransferase AcuA / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


butanediol catabolic process / acetyl-CoA synthetase acetyltransferase activity / carbon catabolite repression of transcription by glucose / acetoin dehydrogenase (NAD+) activity / cellular response to acetate / acetoin catabolic process / spore germination / acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process ...butanediol catabolic process / acetyl-CoA synthetase acetyltransferase activity / carbon catabolite repression of transcription by glucose / acetoin dehydrogenase (NAD+) activity / cellular response to acetate / acetoin catabolic process / spore germination / acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process / sporulation resulting in formation of a cellular spore / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / membrane raft / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Acetoin utilization protein AcuA / 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. / Acetyltransferase (GNAT) family / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily ...Acetoin utilization protein AcuA / 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. / Acetyltransferase (GNAT) family / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Acetyl-coenzyme A synthetase / Acetoin utilization protein AcuA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsZheng LJ / Du Y / Bange G
Funding support Germany, United Kingdom, 4 items
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, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51121.png

Downloads & links

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Map

FileDownload / File: emd_51121.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 352 pix.
= 249.216 Å		0.71 Å/pix.
x 352 pix.
= 249.216 Å		0.71 Å/pix.
x 352 pix.
= 249.216 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.708 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0035
Minimum - Maximum-0.021267273 - 0.03317886
Average (Standard dev.)-0.000008275306 (±0.000573061)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 249.216 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51121_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51121_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AcsA-AcuA complex

EntireName: AcsA-AcuA complex
Components
  • Complex: AcsA-AcuA complex
    • Protein or peptide: Acetyl-coenzyme A synthetase
    • Protein or peptide: Acetoin utilization protein AcuA

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Supramolecule #1: AcsA-AcuA complex

SupramoleculeName: AcsA-AcuA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis (bacteria)

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Macromolecule #1: Acetyl-coenzyme A synthetase

MacromoleculeName: Acetyl-coenzyme A synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: acetate-CoA ligase
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 64.975852 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNLKALPAIE GDHNLKNYEE TYRHFDWAEA EKHFSWHETG KLNAAYEAID RHAESFRKNK VALYYKDAKR DEKYTFKEMK EESNRAGNV LRRYGNVEKG DRVFIFMPRS PELYFIMLGA IKIGAIAGPL FEAFMEGAVK DRLENSEAKV VVTTPELLER I PVDKLPHL ...String:
MNLKALPAIE GDHNLKNYEE TYRHFDWAEA EKHFSWHETG KLNAAYEAID RHAESFRKNK VALYYKDAKR DEKYTFKEMK EESNRAGNV LRRYGNVEKG DRVFIFMPRS PELYFIMLGA IKIGAIAGPL FEAFMEGAVK DRLENSEAKV VVTTPELLER I PVDKLPHL QHVFVVGGEA ESGTNIINYD EAAKQESTRL DIEWMDKKDG FLLHYTSGST GTPKGVLHVH EAMIQQYQTG KW VLDLKEE DIYWCTADPG WVTGTVYGIF APWLNGATNV IVGGRFSPES WYGTIEQLGV NVWYSAPTAF RMLMGAGDEM AAK YDLTSL RHVLSVGEPL NPEVIRWGHK VFNKRIHDTW WMTETGSQLI CNYPCMDIKP GSMGKPIPGV EAAIVDNQGN ELPP YRMGN LAIKKGWPSM MHTIWNNPEK YESYFMPGGW YVSGDSAYMD EEGYFWFQGR VDDVIMTSGE RVGPFEVESK LVEHP AIAE AGVIGKPDPV RGEIIKAFIA LREGFEPSDK LKEEIRLFVK QGLAAHAAPR EIEFKDKLPK TRSGKIMRRV LKAWEL NLP AGDLSTMED

UniProtKB: Acetyl-coenzyme A synthetase

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Macromolecule #2: Acetoin utilization protein AcuA

MacromoleculeName: Acetoin utilization protein AcuA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 24.36275 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEHHKTYHSA NIKTATGSLL IEGPVSPEDL AGYEFHKDLT AFRPPREQHE ALVDIAGLPE GRIIIARDGR TIVGYVTYLY PDPLERWSE GNMEDLIELG AIEVAPDYRG CAVGKTLLTV SMMDEQMENY IVMTTEYYWH WDLKGMKKDV WEYRKIMEKM M NAGGLVWF ...String:
MEHHKTYHSA NIKTATGSLL IEGPVSPEDL AGYEFHKDLT AFRPPREQHE ALVDIAGLPE GRIIIARDGR TIVGYVTYLY PDPLERWSE GNMEDLIELG AIEVAPDYRG CAVGKTLLTV SMMDEQMENY IVMTTEYYWH WDLKGMKKDV WEYRKIMEKM M NAGGLVWF ATDEPEISSH PANCLMARIG KNVSQESIEQ FDRLRFYHRY MY

UniProtKB: Acetoin utilization protein AcuA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2969170
Startup modelType of model: OTHER / Details: alphafold prediction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124994
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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