[English] 日本語
Yorodumi
- PDB-9g7f: Cryo-EM structure of Acetyl-coenzyme A synthetase (AcsA) dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g7f
TitleCryo-EM structure of Acetyl-coenzyme A synthetase (AcsA) dimer
Components
  • Acetoin utilization protein AcuA
  • Acetyl-coenzyme A synthetase
KeywordsBIOSYNTHETIC PROTEIN / Ac-CoA synthetase AcsA / acetate switch / GCN5-related N-acetyltransferase AcuA
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Acetyl-coenzyme A synthetase
A: Acetyl-coenzyme A synthetase
C: Acetoin utilization protein AcuA


Theoretical massNumber of molelcules
Total (without water)154,3143
Polymers154,3143
Non-polymers00
Water00
1


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

-
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
#2: Protein Acetoin utilization protein AcuA / Protein acetyltransferase AcuA


Mass: 24362.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: acuA, BSU29690 / Production host: Escherichia coli (E. coli)
References: UniProt: P39065, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: AcsA-AcuA complex / 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

-
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)

-
Processing

EM softwareName: PHENIX / Version: dev_4620: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2969170
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124994 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049924
ELECTRON MICROSCOPYf_angle_d0.7213446
ELECTRON MICROSCOPYf_dihedral_angle_d4.9211308
ELECTRON MICROSCOPYf_chiral_restr0.0471378
ELECTRON MICROSCOPYf_plane_restr0.0061732

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more