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Structure and reactivity of Bacillus subtilis MenD catalyzing the first committed step in menaquinone biosynthesis.

Dawson A, Chen M, Fyfe PK, Guo Z, Hunter WN - J. Mol. Biol. (2010)

Bottom Line: Arg409 plays a significant role in binding both substrates while Arg428 contributes mainly to binding of alpha-ketoglutarate.Mutagenesis of Phe490 and Ile489 has the most profound influence on catalytic efficiency, indicating that these two residues are important for binding of isochorismate and for stabilizing the cofactor position.These data allow for a detailed description of the structure-reactivity relationship that governs MenD function and refinement of the model for the catalytic intermediate that supports the Stetter-like conjugate addition.

View Article: PubMed Central - PubMed

Affiliation: Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.

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The secondary and domain structure of BsMenD. A ribbon diagram of the enzyme subunit showing the elements of secondary structure with atoms of ThDP depicted as spheres according to atom type: C, gray; N, blue; O, red; S, yellow; P, orange. The N- and C-terminal positions are labeled, as are the elements of secondary structure.
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fig2: The secondary and domain structure of BsMenD. A ribbon diagram of the enzyme subunit showing the elements of secondary structure with atoms of ThDP depicted as spheres according to atom type: C, gray; N, blue; O, red; S, yellow; P, orange. The N- and C-terminal positions are labeled, as are the elements of secondary structure.

Mentions: MenD shows the three-domain architecture typical of ThDP-dependent enzymes (Fig. 2).21 Sequence and structural analyses place MenD in the pyruvate oxidase class of these enzymes, where domain I contains the cofactor pyrimidine-binding motif, domain III binds the diphosphate, and the central domain has variable, often ill-defined, function. In BsMenD, domain I spans approximately the first 190 residues. An ordered linker region leads into domain II, which consists of residues 205–345. A smaller linker then leads into domain III, which starts at approximately residue 355 and continues to the C terminus (Fig. 2). Each domain consists of a parallel β-sheet sandwiched between several α-helices; in BsMenD, the central domain has five strands and there are six in domains I and III.


Structure and reactivity of Bacillus subtilis MenD catalyzing the first committed step in menaquinone biosynthesis.

Dawson A, Chen M, Fyfe PK, Guo Z, Hunter WN - J. Mol. Biol. (2010)

The secondary and domain structure of BsMenD. A ribbon diagram of the enzyme subunit showing the elements of secondary structure with atoms of ThDP depicted as spheres according to atom type: C, gray; N, blue; O, red; S, yellow; P, orange. The N- and C-terminal positions are labeled, as are the elements of secondary structure.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2914249&req=5

fig2: The secondary and domain structure of BsMenD. A ribbon diagram of the enzyme subunit showing the elements of secondary structure with atoms of ThDP depicted as spheres according to atom type: C, gray; N, blue; O, red; S, yellow; P, orange. The N- and C-terminal positions are labeled, as are the elements of secondary structure.
Mentions: MenD shows the three-domain architecture typical of ThDP-dependent enzymes (Fig. 2).21 Sequence and structural analyses place MenD in the pyruvate oxidase class of these enzymes, where domain I contains the cofactor pyrimidine-binding motif, domain III binds the diphosphate, and the central domain has variable, often ill-defined, function. In BsMenD, domain I spans approximately the first 190 residues. An ordered linker region leads into domain II, which consists of residues 205–345. A smaller linker then leads into domain III, which starts at approximately residue 355 and continues to the C terminus (Fig. 2). Each domain consists of a parallel β-sheet sandwiched between several α-helices; in BsMenD, the central domain has five strands and there are six in domains I and III.

Bottom Line: Arg409 plays a significant role in binding both substrates while Arg428 contributes mainly to binding of alpha-ketoglutarate.Mutagenesis of Phe490 and Ile489 has the most profound influence on catalytic efficiency, indicating that these two residues are important for binding of isochorismate and for stabilizing the cofactor position.These data allow for a detailed description of the structure-reactivity relationship that governs MenD function and refinement of the model for the catalytic intermediate that supports the Stetter-like conjugate addition.

View Article: PubMed Central - PubMed

Affiliation: Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.

Show MeSH