New insights into structure–function relationships of oxalyl CoA decarboxylase from Escherichia coli

Abstract

DatabaseStructural data for holo-EcODC (ThDP-EcODC) in the absence of additional ligands and in complex with either ADP or acetyl CoA have been submitted to the Protein Data Bank under the accession numbers 2q27, 2q28 and 2q29, respectively. The gene yfdU from Escherichia coli encodes a putative oxalyl coenzyme A decarboxylase, a thiamine diphosphate-dependent enzyme that is potentially involved in the degradation of oxalate. The enzyme has been purified to homogeneity. The kinetic constants for conversion of the substrate oxalyl coenzyme A by the enzyme in the absence and presence of the inhibitor coenzyme A, as well as in the absence and presence of the activator adenosine 5¢-diphosphate, were determined using a novel continuous optical assay. The effects of these ligands on the solution and crystal structure of the enzyme were studied using small-angle X-ray scattering and X-ray crystal diffraction. Analyses of the obtained crystal structures of the enzyme in complex with the cofactor thiamine diphosphate, the activator adenosine 5¢-diphosphate and the inhibitor acetyl coenzyme A, as well as the corresponding solution scattering patterns, allow comparison of the oligomer structures of the enzyme complexes under various experimental conditions, and provide insights into the architecture of substrate and effector binding sites. Abbreviations EcODC, oxalyl CoA decarboxylase from Escherichia coli; OfODC, oxalyl CoA decarboxylase from Oxalobacter formigenes; PADP, 3¢-phosphoadenosine 5¢-diphosphate; ThDP, thiamine diphosphate.

Modeling time-series data from microbial communities

“…we also found that other OTUs-such as some members of the families S24-7, Helicobacter, and Lachnospiraceae-are more positively affected by oxalate consumption than these well-known oxalate degraders (Tables 1 and 2). One possible explanation is that these taxa have uncharacterized oxalate degrading capacity or homologs of oxalyl-CoA decarboxylase (Sahin, 2003;Werther et al, 2010). Even in strains isolated from N. albigula, Miller et al, (2014) find species that can degrade oxalate in vitro may lack the oxalyl-CoA decarboxylase gene.…”

In Silico Identification of Epitopes in Mycobacterium avium subsp. paratuberculosis Proteins That Were Upregulated under Stress Conditions

“…Similarly, for MAP3651c, template 2CX9 was modeled by SWISS-MODEL Workspace and template 2PGO (L. Chen et al, unpublished data) was modeled by ElliPro. The MAP3523c protein was also modeled with two different templates, 2Q29 (39) by SWISS-MODEL Workspace and 2Q27 (39) by ElliPro, from the crystal structure of oxalyl-coenzyme A (oxalyl-CoA) decarboxylase from E. coli. The details of the 3D structure template IDs and the descriptions of the source molecules are shown in Table S3 in the supplemental material.…”

Allosteric regulation of menaquinone (vitamin K2) biosynthesis in the human pathogen Mycobacterium tuberculosis

“…Others, such as ␣-ketoglutarate dehydrogenase and 2-hydroxy-3-oxoadipate synthase, are allosterically activated by binding of a small molecule (acetyl-CoA) to a shallow pocket on the enzyme surface and allosterically inhibited by binding of a regulatory protein (GarA) (40 -42). Similarly, pyruvate decarboxylase (43), phenylpyruvate decarboxylase (17,18), and oxalyl-CoA decarboxylase (21) have all been shown to be positively regulated by the direct binding of small molecules to domain II.…”