5MZX | pdb_00005mzx

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

• PDB DOI: https://doi.org/10.2210/pdb5MZX/pdb

• Classification: LYASE
• Organism(s): Myxococcus xanthus DK 1622
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-02-02 Released: 2017-05-31 
• Deposition Author(s): Bock, T., Luxenburger, E., Hoffmann, J., Schuetza, V., Feiler, C., Mueller, R., Blankenfeldt, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

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

• PubMed: 28508504 
• DOI: https://doi.org/10.1002/anie.201701992
• Primary Citation 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.

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Organizational Affiliation: 
• Structure and Function of Proteins, Helmholtz Centre for Infection Research, I, nhoffenstr. 7, 38124, Braunschweig, Germany.
Department of Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany.
Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Saarland University, 66123, Saarbrücken, Germany.
Institute of Reconstructive Neurobiology, University Hospital Bonn, University of Bonn, 53127, Bonn, Germany.
Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Straße 15, 12489, Berlin, Germany.
Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 110.8 kDa 
• Atom Count: 8,115 
• Modeled Residue Count: 1,007 
• Deposited Residue Count: 1,026 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaconate CoA-transferase family, subunit A	A, B [auth C]	265	Myxococcus xanthus DK 1622	Mutation(s): 1  Gene Names: MXAN_4264
UniProt
Find proteins for Q1D4I4 (Myxococcus xanthus (strain DK1622)) Explore Q1D4I4  Go to UniProtKB:  Q1D4I4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaconate CoA-transferase family, subunit B	C [auth D], D [auth B]	248	Myxococcus xanthus DK 1622	Mutation(s): 2  Gene Names: MXAN_4265
UniProt
Find proteins for Q1D4I3 (Myxococcus xanthus (strain DK1622)) Explore Q1D4I3  Go to UniProtKB:  Q1D4I3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4PS	K [auth D], N [auth B]	4'-diphospho pantetheine C11 H24 N2 O10 P2 S UQURMDBHCKDEJS-VIFPVBQESA-N
GOL	E [auth A], J [auth C], M [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	F [auth C], G [auth C], H [auth C], I [auth C], L [auth D], O [auth B]	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), 0.197 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.546	α = 90
b = 93.392	β = 103.93
c = 90.044	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Bock, T., Luxenburger, E., Hoffmann, J., Schuetza, V., Feiler, C., Mueller, R., Blankenfeldt, W.

Revision History  

• 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