5MZX

Crystal structure of the decarboxylase AibA/AibB in complex with 4'-diphospho pantetheine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.197 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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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
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  • 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): 2 
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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4PS
Query on 4PS

Download Ideal Coordinates CCD File 
K [auth D],
N [auth B]
4'-diphospho pantetheine
C11 H24 N2 O10 P2 S
UQURMDBHCKDEJS-VIFPVBQESA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
J [auth C],
M [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth C]
G [auth C]
H [auth C]
I [auth C]
L [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.546α = 90
b = 93.392β = 103.93
c = 90.044γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4PSClick on this verticalbar to view details

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