Crystal structure of YisK from Bacillus subtilis in complex with reaction product 4-Hydroxy-2-oxoglutaric acid

Experimental Data Snapshot

  • Resolution: 1.93 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Bacillus subtilis YisK possesses oxaloacetate decarboxylase activity and exhibits Mbl-dependent localization.

Guo, T.Sperber, A.M.Krieger, I.V.Duan, Y.Chemelewski, V.R.Sacchettini, J.C.Herman, J.K.

(2024) J Bacteriol 206: e0020223-e0020223

  • DOI: https://doi.org/10.1128/jb.00202-23
  • Primary Citation of Related Structures:  
    8SKY, 8SUT, 8SUU

  • PubMed Abstract: 

    YisK is an uncharacterized protein in Bacillus subtilis previously shown to interact genetically with the elongasome protein Mbl. YisK overexpression leads to cell widening and lysis, phenotypes that are dependent on mbl and suppressed by mbl mutations. In the present work, we characterize YisK's localization, structure, and enzymatic activity. We show that YisK localizes as puncta that depend on Mbl. YisK belongs to the fumarylacetoacetate hydrolase (FAH) superfamily, and crystal structures revealed close structural similarity to two oxaloacetate (OAA) decarboxylases: human mitochondrial FAHD1 and Corynebacterium glutamicum Cg1458. We demonstrate that YisK can also catalyze the decarboxylation of OAA ( K m = 134 µM, K cat = 31 min -1 ). A catalytic dead variant (YisK E148A, E150A) retains wild-type localization and still widens cells following overexpression, indicating these activities are not dependent on YisK catalysis. Conversely, a non-localizing variant (YisK E30A) retains wild-type enzymatic activity in vitro but localizes diffusely and no longer widens cells following overexpression. Together, these results suggest that YisK may be subject to spatial regulation that depends on the cell envelope synthesis machinery. IMPORTANCE The elongasome is a multiprotein complex that guides lengthwise growth in some bacteria. We previously showed that, in B. subtilis , overexpression of an uncharacterized putative enzyme (YisK) perturbed function of the actin-like elongasome protein Mbl. Here, we show that YisK exhibits Mbl-dependent localization. Through biochemical and structural characterization, we demonstrate that, like its mitochondrial homolog FAHD1, YisK can catalyze the decarboxylation of the oxaloacetate to pyruvate and CO 2 . YisK is the first example of an enzyme implicated in central carbon metabolism with subcellular localization that depends on Mbl.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University , College Station, Texas, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fumarylacetoacetate hydrolase family protein
A, B
312Bacillus subtilisMutation(s): 0 
Gene Names: B4122_0586
Find proteins for O06724 (Bacillus subtilis (strain 168))
Explore O06724 
Go to UniProtKB:  O06724
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06724
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.93 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.686α = 90
b = 93.983β = 90
c = 124.981γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Welch FoundationUnited StatesA-0015

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Database references