9S4V | pdb_00009s4v

AcuB from Bacillus subtilis with AMP and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 
    0.266 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.204 (DCC) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

AcuB senses cellular energy charge to coordinate acetyl-CoA synthesis in bacteria.

Janetzky, M.Geist, N.Schulze, S.Ruckert, H.Gatzemeyer, K.Palm, G.J.Berndt, L.Girbardt, B.Weis, D.Menyes, I.Welsch, N.Schweder, T.Dorr, M.Kemnitz, S.Bornscheuer, U.T.Delcea, M.Lammers, M.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-71006-w
  • Primary Citation Related Structures: 
    9S4V, 9S4W, 9S4X, 9S4Y, 9S4Z, 9S50, 9S51, 9S52

  • PubMed Abstract: 

    Bacteria adjust their metabolism to the cellular energy state. AMP-forming acetyl-CoA-synthetase AcsA generates acetyl-CoA from acetate, ATP and CoA. In Bacilli, including Bacillus subtilis and Geobacillus stearothermophilus, AcsA is reversely transcribed upstream of the acu-operon encoding for the proteins AcuA, AcuB and AcuC. Lysine-acetyltransferase AcuA uses acetyl-CoA to acetylate and inactivate AcsA, while AcuC re-activates AcsA activity by deacetylation. How the counteracting activities of AcuA and AcuC are regulated is not understood. Here, we close this gap of knowledge and perform a structure-function analyzes on AcuB. These reveal AcuB forming a scissor-shaped dimer with each monomer consisting of an N-terminal Bateman domain binding to adenine nucleotides and a C-terminal ACT domain. Structural and biochemical studies as well as molecular dynamics simulations support that AMP bound AcuB binds and inhibits AcuC. Our data describe another layer of regulation of AcsA activity in Firmicutes coordinating acetate assimilation and dissimilation by the energy sensor AcuB.


  • Organizational Affiliation
    • Department of Synthetic and Structural Biochemistry, University of Greifswald, Institute of Biochemistry, Greifswald, Germany.

Macromolecule Content 

  • Total Structure Weight: 78.84 kDa 
  • Atom Count: 5,267 
  • Modeled Residue Count: 641 
  • Deposited Residue Count: 672 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetoin utilization protein AcuB
A, B, C
224Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: acuBBSU29700
UniProt
Find proteins for P39066 (Bacillus subtilis (strain 168))
Explore P39066 
Go to UniProtKB:  P39066
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39066
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free:  0.266 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.204 (DCC) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.305α = 90
b = 79.779β = 90
c = 153.788γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-25
    Type: Initial release
  • Version 1.1: 2026-05-20
    Changes: Database references