Formyl‐coenzyme A (CoA):oxalate CoA‐transferase from the acidophile <i>Acetobacter aceti</i> has a distinctive electrostatic surface and inherent acid stability

Mullins, E.A.; Starks, Courtney M.; Francois, Julie A.; Sael, Lee; Kappock, T.J.

doi:10.1002/pro.2054

Cited by 19 publications

(20 citation statements)

References 67 publications

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“…A previously described high performance liquid chromatography (HPLC) method [23], [25] was used to identify substrates for YfdE and UctC. Candidate substrate pairs were incubated with enzyme, then acid-quenched and analyzed by HPLC (Figure 3).…”

Section: Resultsmentioning

confidence: 99%

“…PDB entries are 4hl6 (white), 4ed9 (dark blue), 1p5h (green) [69], 1pt7 (cyan) [24], 3ubm (orange) [25], 1×k7 (yellow) [70], 1×74 (magenta) [71], and 2g04 (pink) [72]. (B) ML phylogram of the structure-based sequence alignment (Figure S6) that corresponds to panel A. UniProt accession numbers and PDB entry codes are given for each taxon.…”

Section: Resultsmentioning

confidence: 99%

“…In these environments, oxalate would be activated for decarboxylation by UctB (FCOCT), which appears to be constitutively expressed in A. aceti strain 1023 [25]. There may also be an endogenous source of oxalate: the acetic acid bacterium Gluconobacter oxydans was reported to form oxalate from glyoxylate [32] but glyoxylate oxidase (EC 1.2.3.5) is presently unassociated with any gene [33].…”

Section: Discussionmentioning

confidence: 99%

“…YfdE, YfdW, and other class III CoA-transferases have considerable sequence divergence, consistent with differing enzymatic functions. While members of the ACOCT family support both ACOCT and FCOCT activities (the latter with reduced specific activity), no member of the FCOCT family supports ACOCT activity [12], [25], [45]. The eight structurally characterized members of the class III CoA-transferase superfamily represent at least four families (Figure 5 and Figure S6), including some with no assigned functions.…”

Section: Discussionmentioning

confidence: 99%

“…Formyl-CoA was synthesized as described previously [25]. DNA modifying enzymes were from New England Biolabs.…”

Section: Methodsmentioning

confidence: 99%

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Function and X-Ray crystal structure of Escherichia coli YfdE

2013

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Many food plants accumulate oxalate, which humans absorb but do not metabolize, leading to the formation of urinary stones. The commensal bacterium Oxalobacter formigenes consumes oxalate by converting it to oxalyl-CoA, which is decarboxylated by oxalyl-CoA decarboxylase (OXC). OXC and the class III CoA-transferase formyl-CoA:oxalate CoA-transferase (FCOCT) are widespread among bacteria, including many that have no apparent ability to degrade or to resist external oxalate. The EvgA acid response regulator activates transcription of the Escherichia coli yfdXWUVE operon encoding YfdW (FCOCT), YfdU (OXC), and YfdE, a class III CoA-transferase that is 30% identical to YfdW. YfdW and YfdU are necessary and sufficient for oxalate-induced protection against a subsequent acid challenge; neither of the other genes has a known function. We report the purification, in vitro characterization, 2.1-Å crystal structure, and functional assignment of YfdE. YfdE and UctC, an orthologue from the obligate aerobe Acetobacter aceti, perform the reversible conversion of acetyl-CoA and oxalate to oxalyl-CoA and acetate. The annotation of YfdE as acetyl-CoA:oxalate CoA-transferase (ACOCT) expands the scope of metabolic pathways linked to oxalate catabolism and the oxalate-induced acid tolerance response. FCOCT and ACOCT active sites contain distinctive, conserved active site loops (the glycine-rich loop and the GNxH loop, respectively) that appear to encode substrate specificity.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…Formyl-CoA was synthesized as described previously [25]. DNA modifying enzymes were from New England Biolabs.…”

Section: Methodsmentioning

confidence: 99%

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Function and X-Ray crystal structure of Escherichia coli YfdE

2013

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Redefining the coenzyme A transferase superfamily with a large set of manually annotated proteins

Hackmann

2022

Protein Science

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The coenzyme A (CoA) transferases are a superfamily of proteins central to the metabolism of acetyl-CoA and other CoA thioesters. They are diverse group, catalyzing over a 100 biochemical reactions and spanning all three domains of life. A deeply rooted idea, proposed two decades ago, is these enzymes fall into three families (I, II, and III). Here we find they fall into different families, which we achieve by analyzing all CoA transferases characterized to date. We manually annotated 94 CoA transferases with functional information (including rates of catalysis for 208 reactions) from 97 publications. This represents all enzymes we could find in the primary literature, and it is double the number annotated in four protein databases (BRENDA, KEGG, MetaCyc, UniProt). We found family I transferases are not closely related to each other in terms of sequence, structure, and reactions catalyzed. This family is not even monophyletic. These problems are solved by regrouping the three families into six, including one family with many non-CoA transferases. The problem (and solution) became apparent only by analyzing our large set of manually annotated proteins. It would have been missed if we had used the small number of proteins annotated in UniProt and other databases. Our work is important to understanding the biology of CoA transferases. It also warns investigators doing phylogenetic analyses of proteins to go beyond information in databases.

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