5E7Q

Acyl-CoA synthetase PtmA2 from Streptomyces platensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Natural separation of the acyl-CoA ligase reaction results in a non-adenylating enzyme.

Wang, N.Rudolf, J.D.Dong, L.B.Osipiuk, J.Hatzos-Skintges, C.Endres, M.Chang, C.Y.Babnigg, G.Joachimiak, A.Phillips, G.N.Shen, B.

(2018) Nat. Chem. Biol. 14: 730-737

  • DOI: 10.1038/s41589-018-0061-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Acyl-coenzyme A (CoA) ligases catalyze the activation of carboxylic acids via a two-step reaction of adenylation followed by thioesterification. Here, we report the discovery of a non-adenylating acyl-CoA ligase PtmA2 and the functional separation of ...

    Acyl-coenzyme A (CoA) ligases catalyze the activation of carboxylic acids via a two-step reaction of adenylation followed by thioesterification. Here, we report the discovery of a non-adenylating acyl-CoA ligase PtmA2 and the functional separation of an acyl-CoA ligase reaction. Both PtmA1 and PtmA2, two acyl-CoA ligases from the biosynthetic pathway of platensimycin and platencin, are necessary for the two steps of CoA activation. Gene inactivation of ptmA1 and ptmA2 resulted in the accumulation of free acid and adenylate intermediates, respectively. Enzymatic and structural characterization of PtmA2 confirmed its ability to only catalyze thioesterification. Structural characterization of PtmA2 revealed it binds both free acid and adenylate substrates and undergoes the established mechanism of domain alternation. Finally, site-directed mutagenesis restored both the adenylation and complete CoA activation reactions. This study challenges the currently accepted paradigm of adenylating enzymes and inspires future investigations on functionally separated acyl-CoA ligases and their ramifications in biology.


    Organizational Affiliation

    Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA. shenb@scripps.edu.,Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA. shenb@scripps.edu.,Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL, USA. shenb@scripps.edu.,Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.,Department of Biosciences, Rice University, Houston, TX, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
acyl-CoA synthetase
A, B
524Streptomyces platensisMutation(s): 2 
Find proteins for A0A0A0V031 (Streptomyces platensis)
Go to UniProtKB:  A0A0A0V031
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.872α = 90.00
b = 146.892β = 90.00
c = 146.928γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
HKL-3000data reduction
PDB_EXTRACTdata extraction
HKL-3000phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM094585

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-10-28
    Type: Database references, Structure summary
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Derived calculations
  • Version 1.3: 2018-07-11
    Type: Data collection, Database references