Kinetic and Mechanistic Characterization of the Formyl-CoA Transferase from Oxalobacter formigenes

Jónsson, S.; Ricagno, Stéfano; Lindqvist, Ylva; Richards, Nigel G. J.

doi:10.1074/jbc.m404873200

Cited by 54 publications

(100 citation statements)

References 56 publications

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“…After injection, the proportion of Buffer G was raised to 6% over a 12-min period followed by a step to 95% Buffer G that was continued for 2 min before returning to 2% Buffer G. Under these conditions ThDP eluted after 3.7 min, oxalyl-CoA eluted after 6.1 min, free CoA eluted after 9.9 min, and formyl-CoA eluted after 11.3 min. The concentration of CoA derivatives in the aliquots was determined as described previously (14).…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…Oxalyl-CoA was synthesized and purified following literature protocols (14,37) and diluted in 50 mM NaH 2 PO 4 , pH 4.5. The reaction was quenched by adding 11.1 l of 20% acetic acid to assay mixture, and the initial rate of formyl-CoA formation was analyzed by reverse-phase HPLC using a modification of a previously published procedure (14). Briefly, 75-l aliquots of quenched reaction mixture were injected onto a C 18 analytical column (Dynamax Microsorb 60 -8 C 18 , 250 ϫ 4.6 mm) equilibrated with 98% Buffer F (25 mM sodium acetate, pH 4.5) and 2% Buffer G (20% Buffer F; 80% CH 3 CN) at a flow rate of 1 ml/min.…”

Section: Methodsmentioning

confidence: 99%

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Structural Basis for Activation of the Thiamin Diphosphate-dependent Enzyme Oxalyl-CoA Decarboxylase by Adenosine Diphosphate

Berthold

Moussatche

Richards

et al. 2005

Journal of Biological Chemistry

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Oxalyl-coenzyme A decarboxylase is a thiamin diphosphate-dependent enzyme that plays an important role in the catabolism of the highly toxic compound oxalate. We have determined the crystal structure of the enzyme from Oxalobacter formigenes from a hemihedrally twinned crystal to 1.73 Å resolution and characterized the steady-state kinetic behavior of the decarboxylase. The monomer of the tetrameric enzyme consists of three ␣/␤-type domains, commonly seen in this class of enzymes, and the thiamin diphosphatebinding site is located at the expected subunit-subunit interface between two of the domains with the cofactor bound in the conserved V-conformation. Although oxalyl-CoA decarboxylase is structurally homologous to acetohydroxyacid synthase, a molecule of ADP is bound in a region that is cognate to the FAD-binding site observed in acetohydroxyacid synthase and presumably fulfils a similar role in stabilizing the protein structure. This difference between the two enzymes may have physiological importance since oxalyl-CoA decarboxylation is an essential step in ATP generation in O. formigenes, and the decarboxylase activity is stimulated by exogenous ADP. Despite the significant degree of structural conservation between the two homologous enzymes and the similarity in catalytic mechanism to other thiamin diphosphate-dependent enzymes, the active site residues of oxalyl-CoA decarboxylase are unique. A suggestion for the reaction mechanism of the enzyme is presented.Oxalic acid is one of nature's most highly oxidized organic compounds, and its dianion is a strong chelator of metal cations, especially Ca 2ϩ , causing oxalate to be highly toxic to many organisms (1). In humans, elevated levels of oxalate are associated with several diseases, including the formation of calcium oxalate stones in the kidney (urolithiasis), renal failure, cardiomyopathy, and cardiac conductance disorders (1-3). Relatively large amounts of oxalate are introduced into the body through the diet, although this diacid may also arise as a byproduct of normal cellular metabolism (4). Because humans, in common with other mammals, are not able to degrade oxalate, this compound must be eliminated by excretion in the urine or via the intestine (5). The recent observation that a symbiotic, gut-dwelling bacterium, Oxalobacter formigenes, may regulate oxalate homeostasis in humans, therefore, has important implications for efforts to develop new strategies for treating oxalate-related diseases (6). O. formigenes is an obligate anaerobe bacterium found in the gastrointestinal tracts of vertebrates, including humans, and is unusual in that it employs oxalate as the sole energy source for its survival (7,8). As a result, this bacterium not only degrades free oxalate entering the intestine lumen but also creates a transepithelial gradient favoring oxalate secretion and preventing absorption of oxalic acid in the lower tract of the intestine (9). A direct correlation between the number of recurrent kidney stone episodes and a lack of O. formigenes in the ...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Structural Basis for Activation of the Thiamin Diphosphate-dependent Enzyme Oxalyl-CoA Decarboxylase by Adenosine Diphosphate

Berthold

Moussatche

Richards

et al. 2005

Journal of Biological Chemistry

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“…Type III CoA transferases, such as the crotonoyl-CoA ( caiB ) and yfdW gene products from E. coli (19)(20)(21) as well as the formyl-CoA transferase (FRC) from Oxalobacter formigenes ( 22 ), share a conserved Asp 169 residue (D169 formyl CoA) involved in catalytic formation of oxo-acid mixed anhydrides as well as covalent CoA thioesters. The baiF and baiK gene products share this conserved residue ( Fig.…”

Section: Cloning Expression and Purifi Cation Of Bile Acid Coa Tranmentioning

confidence: 99%

Identification and characterization of two bile acid coenzyme A transferases from Clostridium scindens, a bile acid 7α-dehydroxylating intestinal bacterium

Ridlon

Hylemon

2012

Journal of Lipid Research

115

109

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“…The arrangement of residues in the cleft of FAR is quite similar to that of M. tuberculosis MCR 13 and other family III CoA transferase members, suggesting that the clefts of FAR would be suitable for substrate binding and catalytic reaction, as observed in the structure of the FRC-CoA complex. 25,28 Functional and structural similarities to other proteins. The multiple alignment of amino acid sequence identities between FAR and FRC or YfdW, as the known structure of the family III CoA transferases, were 29.8% and 32.7%, respectively [Fig 2(A)].…”

Section: Structural Comparisonmentioning

confidence: 99%

Crystal structure of fatty acid‐CoA racemase from Mycobacterium tuberculosis H37Rv

et al. 2006

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Kinetic and Mechanistic Characterization of the Formyl-CoA Transferase from Oxalobacter formigenes

Cited by 54 publications

References 56 publications

Structural Basis for Activation of the Thiamin Diphosphate-dependent Enzyme Oxalyl-CoA Decarboxylase by Adenosine Diphosphate

Structural Basis for Activation of the Thiamin Diphosphate-dependent Enzyme Oxalyl-CoA Decarboxylase by Adenosine Diphosphate

Identification and characterization of two bile acid coenzyme A transferases from Clostridium scindens, a bile acid 7α-dehydroxylating intestinal bacterium

Crystal structure of fatty acid‐CoA racemase from Mycobacterium tuberculosis H37Rv

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