Tri-functional propionyl-CoA synthase of Erythrobacter sp. NAP1 with bound NADP+ and phosphomethylphosphonic acid adenylate ester

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


The multicatalytic compartment of propionyl-CoA synthase sequesters a toxic metabolite.

Bernhardsgrutter, I.Vogeli, B.Wagner, T.Peter, D.M.Cortina, N.S.Kahnt, J.Bange, G.Engilberge, S.Girard, E.Riobe, F.Maury, O.Shima, S.Zarzycki, J.Erb, T.J.

(2018) Nat Chem Biol 14: 1127-1132

  • DOI: https://doi.org/10.1038/s41589-018-0153-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Cells must cope with toxic or reactive intermediates formed during metabolism. One coping strategy is to sequester reactions that produce such intermediates within specialized compartments or tunnels connecting different active sites. Here, we show that propionyl-CoA synthase (PCS), an ∼ 400-kDa homodimer, three-domain fusion protein and the key enzyme of the 3-hydroxypropionate bi-cycle for CO 2 fixation, sequesters its reactive intermediate acrylyl-CoA. Structural analysis showed that PCS forms a multicatalytic reaction chamber. Kinetic analysis suggested that access to the reaction chamber and catalysis are synchronized by interdomain communication. The reaction chamber of PCS features three active sites and has a volume of only 33 nm 3 . As one of the smallest multireaction chambers described in biology, PCS may inspire the engineering of a new class of dynamically regulated nanoreactors.

  • Organizational Affiliation

    Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetyl-coenzyme A synthetase
A, B
1,850Erythrobacter sp. NAP1Mutation(s): 0 
Gene Names: NAP1_02725
Find proteins for A3WE14 (Erythrobacter sp. NAP1)
Explore A3WE14 
Go to UniProtKB:  A3WE14
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3WE14
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 383.414α = 90
b = 86.74β = 108.89
c = 133.958γ = 90
Software Package:
Software NamePurpose
MOSFLMdata collection
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.3: 2018-11-28
    Changes: Data collection, Database references