4MZQ

beta-Alanyl-CoA:Ammonia Lyase from Clostridium propionicum in complex with propionyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.587 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High resolution crystal structure of Clostridium propionicum beta-alanyl-CoA:ammonia lyase, a new member of the "hot dog fold" protein superfamily.

Heine, A.Herrmann, G.Selmer, T.Terwesten, F.Buckel, W.Reuter, K.

(2014) Proteins 82: 2041-2053

  • DOI: 10.1002/prot.24557
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Clostridium propionicum is the only organism known to ferment β-alanine, a constituent of coenzyme A (CoA) and the phosphopantetheinyl prosthetic group of holo-acyl carrier protein. The first step in the fermentation is a CoA-transfer to β-alanine. S ...

    Clostridium propionicum is the only organism known to ferment β-alanine, a constituent of coenzyme A (CoA) and the phosphopantetheinyl prosthetic group of holo-acyl carrier protein. The first step in the fermentation is a CoA-transfer to β-alanine. Subsequently, the resulting β-alanyl-CoA is deaminated by the enzyme β-alanyl-CoA:ammonia lyase (Acl) to reversibly form ammonia and acrylyl-CoA. We have determined the crystal structure of Acl in its apo-form at a resolution of 0.97 Å as well as in complex with CoA at a resolution of 1.59 Å. The structures reveal that the enyzme belongs to a superfamily of proteins exhibiting a so called "hot dog fold" which is characterized by a five-stranded antiparallel β-sheet with a long α-helix packed against it. The functional unit of all "hot dog fold" proteins is a homodimer containing two equivalent substrate binding sites which are established by the dimer interface. In the case of Acl, three functional dimers combine to a homohexamer strongly resembling the homohexamer formed by YciA-like acyl-CoA thioesterases. Here, we propose an enzymatic mechanism based on the crystal structure of the Acl·CoA complex and molecular docking.


    Organizational Affiliation

    Institut für Pharmazeutische Chemie, Fachbereich Pharmazie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032, Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
beta-Alanyl-CoA:Ammonia Lyase
A, B, C, D, E, F, G, H, I, J, K, L
144Anaerotignum propionicumMutation(s): 0 
Gene Names: acl2
Find proteins for Q6KC22 (Anaerotignum propionicum)
Go to UniProtKB:  Q6KC22
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1VU
Query on 1VU

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
propionyl Coenzyme A
C24 H40 N7 O17 P3 S
QAQREVBBADEHPA-IEXPHMLFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.587 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.520α = 90.00
b = 110.965β = 89.98
c = 115.370γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-09-30 
  • Released Date: 2014-03-26 
  • Deposition Author(s): Heine, A., Reuter, K.

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2014-06-11
    Type: Database references
  • Version 1.2: 2014-09-03
    Type: Database references