6EQO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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


This is version 1.3 of the entry. See complete history


Literature

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: 10.1038/s41589-018-0153-x
  • Structures With Same Primary Citation

  • 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 t ...

    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. toerb@mpi-marburg.mpg.de.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetyl-coenzyme A synthetaseA, B1850Erythrobacter sp. NAP1Mutation(s): 0 
Gene Names: NAP1_02725
Find proteins for A3WE14 (Erythrobacter sp. NAP1)
Explore A3WE14 
Go to UniProtKB:  A3WE14
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
ACP
Query on ACP

Download CCD File 
A, B
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
MOSFLMdata collection
Aimlessdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Germany--

Revision History 

  • 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