5N03

Crystal structure of the decarboxylase AibA/AibB C56V variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

AibA/AibB Induces an Intramolecular Decarboxylation in Isovalerate Biosynthesis by Myxococcus xanthus.

Bock, T.Luxenburger, E.Hoffmann, J.Schutza, V.Feiler, C.Muller, R.Blankenfeldt, W.

(2017) Angew Chem Int Ed Engl 56: 9986-9989

  • DOI: https://doi.org/10.1002/anie.201701992
  • Primary Citation of Related Structures:  
    5MZW, 5MZX, 5MZY, 5MZZ, 5N00, 5N01, 5N02, 5N03

  • PubMed Abstract: 

    Isovaleryl coenzyme A (IV-CoA) is an important precursor for iso-fatty acids and lipids. It acts in the development of myxobacteria, which can produce this compound from acetyl-CoA through alternative IV-CoA biosynthesis (aib). A central reaction of aib is catalyzed by AibA/AibB, which acts as a cofactor-free decarboxylase despite belonging to the family of CoA-transferases. We developed an efficient expression system for AibA/AibB that allowed the determination of high-resolution crystal structures in complex with different ligands. Through mutational studies, we show that an active-site cysteine previously proposed to be involved in decarboxylation is not required for activity. Instead, AibA/AibB seems to induce an intramolecular decarboxylation by binding its substrate in a hydrophobic cavity and forcing it into a bent conformation. Our study opens opportunities for synthetic biology studies, since AibA/AibB may be suitable for the production of isobutene, a precursor of biofuels and chemicals.


  • Organizational Affiliation

    Structure and Function of Proteins, Helmholtz Centre for Infection Research, I, nhoffenstr. 7, 38124, Braunschweig, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutaconate CoA-transferase family, subunit AA,
B [auth C]
265Myxococcus xanthus DK 1622Mutation(s): 1 
Gene Names: MXAN_4264
UniProt
Find proteins for Q1D4I4 (Myxococcus xanthus (strain DK1622))
Explore Q1D4I4 
Go to UniProtKB:  Q1D4I4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1D4I4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutaconate CoA-transferase family, subunit BC [auth D],
D [auth B]
248Myxococcus xanthus DK 1622Mutation(s): 3 
Gene Names: MXAN_4265
UniProt
Find proteins for Q1D4I3 (Myxococcus xanthus (strain DK1622))
Explore Q1D4I3 
Go to UniProtKB:  Q1D4I3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1D4I3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.999α = 90
b = 93.246β = 104.41
c = 91.061γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-08-09
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description