8RPL

AMP-forming acetyl-CoA synthetase from Chloroflexota bacterium with bound acetyl AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.161 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

Acetyl-CoA synthetase activity is enzymatically regulated by lysine acetylation using acetyl-CoA or acetyl-phosphate as donor molecule.

Qin, C.Graf, L.G.Striska, K.Janetzky, M.Geist, N.Specht, R.Schulze, S.Palm, G.J.Girbardt, B.Dorre, B.Berndt, L.Kemnitz, S.Doerr, M.Bornscheuer, U.T.Delcea, M.Lammers, M.

(2024) Nat Commun 15: 6002-6002

  • DOI: https://doi.org/10.1038/s41467-024-49952-0
  • Primary Citation of Related Structures:  
    8RPK, 8RPL

  • PubMed Abstract: 

    The AMP-forming acetyl-CoA synthetase is regulated by lysine acetylation both in bacteria and eukaryotes. However, the underlying mechanism is poorly understood. The Bacillus subtilis acetyltransferase AcuA and the AMP-forming acetyl-CoA synthetase AcsA form an AcuA•AcsA complex, dissociating upon lysine acetylation of AcsA by AcuA. Crystal structures of AcsA from Chloroflexota bacterium in the apo form and in complex with acetyl-adenosine-5'-monophosphate (acetyl-AMP) support the flexible C-terminal domain adopting different conformations. AlphaFold2 predictions suggest binding of AcuA stabilizes AcsA in an undescribed conformation. We show the AcuA•AcsA complex dissociates upon acetyl-coenzyme A (acetyl-CoA) dependent acetylation of AcsA by AcuA. We discover an intrinsic phosphotransacetylase activity enabling AcuA•AcsA generating acetyl-CoA from acetyl-phosphate (AcP) and coenzyme A (CoA) used by AcuA to acetylate and inactivate AcsA. Here, we provide mechanistic insights into the regulation of AMP-forming acetyl-CoA synthetases by lysine acetylation and discover an intrinsic phosphotransacetylase allowing modulation of its activity based on AcP and CoA levels.


  • Organizational Affiliation

    Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetate--CoA ligase
A, B, C, D
657Chloroflexota bacteriumMutation(s): 0 
Gene Names: acsE6J36_13485
EC: 6.2.1.1
UniProt
Find proteins for A0A535FEC2 (Chloroflexota bacterium)
Explore A0A535FEC2 
Go to UniProtKB:  A0A535FEC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A535FEC2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6R9 (Subject of Investigation/LOI)
Query on 6R9

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate
C12 H16 N5 O8 P
UBPVOHPZRZIJHM-WOUKDFQISA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
P [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
NEP
Query on NEP
A, B, C, D
L-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.161 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.909α = 90
b = 161.909β = 90
c = 817.234γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
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: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-07-31
    Changes: Database references