9S50 | pdb_00009s50

AcuB from Geobacillus stearothermophilus with AMP and ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 
    0.287 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.225 (DCC) 

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

Validation slider image for 9S50

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: 51.48 kDa 
  • Atom Count: 3,271 
  • Modeled Residue Count: 401 
  • Deposited Residue Count: 446 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AcuB from Geobacillus stearothermophilus
A, B
223Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
G [auth B],
H [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
I [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
(Subject of Investigation/LOI)

Query on CL



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free:  0.287 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.225 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.564α = 90
b = 96.535β = 90
c = 101.435γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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