4C3S

Structure of a propionaldehyde dehydrogenase from the Clostridium phytofermentans fucose utilisation bacterial microcompartment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Insight Into Coenzyme a Cofactor Binding and the Mechanism of Acyl-Transfer in an Acylating Aldehyde Dehydrogenase from Clostridium Phytofermentans.

Tuck, L.R.Altenbach, K.Ang, T.F.Crawshaw, A.D.Campopiano, D.J.Clarke, D.J.Marles-Wright, J.

(2016) Sci.Rep. 6: 22108

  • DOI: 10.1038/srep22108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The breakdown of fucose and rhamnose released from plant cell walls by the cellulolytic soil bacterium Clostridium phytofermentans produces toxic aldehyde intermediates. To enable growth on these carbon sources, the pathway for the breakdown of fucos ...

    The breakdown of fucose and rhamnose released from plant cell walls by the cellulolytic soil bacterium Clostridium phytofermentans produces toxic aldehyde intermediates. To enable growth on these carbon sources, the pathway for the breakdown of fucose and rhamnose is encapsulated within a bacterial microcompartment (BMC). These proteinaceous organelles sequester the toxic aldehyde intermediates and allow the efficient action of acylating aldehyde dehydrogenase enzymes to produce an acyl-CoA that is ultimately used in substrate-level phosphorylation to produce ATP. Here we analyse the kinetics of the aldehyde dehydrogenase enzyme from the fucose/rhamnose utilisation BMC with different short-chain fatty aldehydes and show that it has activity against substrates with up to six carbon atoms, with optimal activity against propionaldehyde. We have also determined the X-ray crystal structure of this enzyme in complex with CoA and show that the adenine nucleotide of this cofactor is bound in a distinct pocket to the same group in NAD(+). This work is the first report of the structure of CoA bound to an aldehyde dehydrogenase enzyme and our crystallographic model provides important insight into the differences within the active site that distinguish the acylating from non-acylating aldehyde dehydrogenase enzymes.


    Organizational Affiliation

    Institute of Quantitative Biology, Biochemistry and Biotechnology, The University of Edinburgh, Max Born Crescent, EH9 3BF, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALDEHYDE DEHYDROGENASE
A
445Lachnoclostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)Mutation(s): 0 
Find proteins for A9KN57 (Lachnoclostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg))
Go to UniProtKB:  A9KN57
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.146 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 138.488α = 90.00
b = 138.488β = 90.00
c = 84.610γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2013-09-25
    Type: Atomic model, Other
  • Version 1.2: 2016-04-20
    Type: Database references
  • Version 1.3: 2019-05-08
    Type: Data collection, Experimental preparation, Other