8SKY

Crystal structure of YisK from Bacillus subtilis in complex with oxalate

Summary for 8SKY

• Entry DOI: 10.2210/pdb8sky/pdb
• Descriptor: Fumarylacetoacetate hydrolase family protein, OXALATE ION, MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: fumarylacetoacetate hydrolase, decarboxylase, elongasome, hydrolase
• Biological source: Bacillus subtilis
• Total number of polymer chains: 2
• Total formula weight: 69386.80

Authors

Krieger, I.V.,Chemelewski, V.,Guo, T.,Sperber, A.,Herman, J.,Sacchettini, J.C. (deposition date: 2023-04-20, release date: 2023-11-01, Last modification date: 2024-02-07)

Primary citation

Guo, T.,Sperber, A.M.,Krieger, I.V.,Duan, Y.,Chemelewski, V.R.,Sacchettini, J.C.,Herman, J.K.
Bacillus subtilis YisK possesses oxaloacetate decarboxylase activity and exhibits Mbl-dependent localization.
J.Bacteriol., 206:e0020223-e0020223, 2024

PubMed Abstract: YisK is an uncharacterized protein in previously shown to interact genetically with the elongasome protein Mbl. YisK overexpression leads to cell widening and lysis, phenotypes that are dependent on and suppressed by 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 Cg1458. We demonstrate that YisK can also catalyze the decarboxylation of OAA ( = 134 µM, = 31 min). 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 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 , 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. YisK is the first example of an enzyme implicated in central carbon metabolism with subcellular localization that depends on Mbl.

PubMed: 38047707
DOI: 10.1128/jb.00202-23

Experimental method

X-RAY DIFFRACTION (2.4 Å)