Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.96 
• Atom Count: 6931 
• Residue Count: 431 
• Unique protein chains: 1

5DBV

Structure of a C269A mutant of propionaldehyde dehydrogenase from the Clostridium phytofermentans fucose utilisation bacterial microcompartment

• DOI: 10.2210/pdb5DBV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-08-22 Released: 2016-03-16 
• Deposition Author(s): Tuck, L.R., Altenbach, K., Ang, T.F., Crawshaw, A.D., Campopiano, D.J., Clarke, D.J., Marles-Wright, J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.183 
• R-Value Work: 0.146 
• R-Value Observed: 0.148 

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: 22108-22108

• PubMed: 26899032 
• DOI: 10.1038/srep22108
• Structures With Same Primary Citation


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Aldehyde Dehydrogenase	A	445	Clostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)	Mutation(s): 1  Gene Names: Cphy_1178
Find proteins for A9KN57 (Lachnoclostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)) Go to UniProtKB:  A9KN57

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	A	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.183 
• R-Value Work: 0.146 
• R-Value Observed: 0.148 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.264	α = 90
b = 138.264	β = 90
c = 84.445	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-08-22 
• Released Date: 2016-03-16 
Deposition Author(s): Tuck, L.R., Altenbach, K., Ang, T.F., Crawshaw, A.D., Campopiano, D.J., Clarke, D.J., Marles-Wright, J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M010996/1

Revision History 

• Version 1.0: 2016-03-16
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Author supporting evidence
• Version 1.2: 2018-01-10
  Changes: Source and taxonomy