7VEE

The ligand-free structure of GfsA KSQ-AT didomain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


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Literature

Structural Insight into the Reaction Mechanism of Ketosynthase-Like Decarboxylase in a Loading Module of Modular Polyketide Synthases.

Chisuga, T.Nagai, A.Miyanaga, A.Goto, E.Kishikawa, K.Kudo, F.Eguchi, T.

(2022) ACS Chem Biol 

  • DOI: 10.1021/acschembio.1c00856
  • Primary Citation of Related Structures:  
    7VEE, 7VEF

  • PubMed Abstract: 
  • Ketosynthase-like decarboxylase (KS Q ) domains are widely distributed in the loading modules of modular polyketide synthases (PKSs) and are proposed to catalyze the decarboxylation of a malonyl or methylmalonyl unit for the construction of the PKS starter unit ...

    Ketosynthase-like decarboxylase (KS Q ) domains are widely distributed in the loading modules of modular polyketide synthases (PKSs) and are proposed to catalyze the decarboxylation of a malonyl or methylmalonyl unit for the construction of the PKS starter unit. KS Q domains have high sequence similarity to ketosynthase (KS) domains, which catalyze transacylation and decarboxylative condensation in polyketide and fatty acid biosynthesis, except that the catalytic Cys residue of KS domains is replaced by Gln in KS Q domains. Here, we present biochemical analyses of GfsA KS Q and CmiP4 KS Q , which are involved in the biosynthesis of FD-891 and cremimycin, respectively. In vitro analysis showed that these KS Q domains catalyze the decarboxylation of malonyl and methylmalonyl units. Furthermore, we determined the crystal structure of GfsA KS Q in complex with a malonyl thioester substrate analogue, which enabled identification of key amino acid residues involved in the decarboxylation reaction. The importance of these residues was confirmed by mutational analysis. On the basis of these findings, we propose a mechanism of the decarboxylation reaction catalyzed by GfsA KS Q . GfsA KS Q initiates decarboxylation by fixing the substrate in a suitable conformation for decarboxylation. The formation of enolate upon decarboxylation is assisted by two conserved threonine residues. Comparison of the structure of GfsA KS Q with those of KS domains suggests that the Gln residue in the active site of the KS Q domain mimics the acylated Cys residue in the active site of KS domains.


    Organizational Affiliation

    Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polyketide synthaseA921Streptomyces graminofaciensMutation(s): 0 
Gene Names: gfsA
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 230.763α = 90
b = 230.763β = 90
c = 117.95γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan20H02911

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release