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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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ThDP interactions with BsMenD. Atoms are colored as follows: C of ThDP, black; C of protein, gray for subunits A and B; P, orange; N, blue; O, red; S, yellow; Mn2+, purple. Purple continuous lines represent coordination of the transition metal ion, and black broken black lines represent potential hydrogen-bonding interactions.
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fig5: ThDP interactions with BsMenD. Atoms are colored as follows: C of ThDP, black; C of protein, gray for subunits A and B; P, orange; N, blue; O, red; S, yellow; Mn2+, purple. Purple continuous lines represent coordination of the transition metal ion, and black broken black lines represent potential hydrogen-bonding interactions.

Mentions: Dimerization is essential for formation of the cofactor binding and active site, with residues from domain I of subunit A and domain III from subunit B forming one site (and vice versa, leading to two active sites per dimer, Fig. 3). A metal cation, assigned as Mn2+, is bound and helps to position the diphosphate group of ThDP and so tether one part of the cofactor to the protein. This is a common feature of ThDP binding and similar to what is observed in EcMenD.15 In BsMenD, the side chains of Asp457 and Asn484, the main-chain carbonyl of Gly486, a water molecule, and two oxygen atoms from the diphosphate group form an octahedral coordination sphere about the metal ion (Fig. 5).


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)

ThDP interactions with BsMenD. Atoms are colored as follows: C of ThDP, black; C of protein, gray for subunits A and B; P, orange; N, blue; O, red; S, yellow; Mn2+, purple. Purple continuous lines represent coordination of the transition metal ion, and black broken black lines represent potential hydrogen-bonding interactions.
© Copyright Policy
Related In: Results  -  Collection

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

fig5: ThDP interactions with BsMenD. Atoms are colored as follows: C of ThDP, black; C of protein, gray for subunits A and B; P, orange; N, blue; O, red; S, yellow; Mn2+, purple. Purple continuous lines represent coordination of the transition metal ion, and black broken black lines represent potential hydrogen-bonding interactions.
Mentions: Dimerization is essential for formation of the cofactor binding and active site, with residues from domain I of subunit A and domain III from subunit B forming one site (and vice versa, leading to two active sites per dimer, Fig. 3). A metal cation, assigned as Mn2+, is bound and helps to position the diphosphate group of ThDP and so tether one part of the cofactor to the protein. This is a common feature of ThDP binding and similar to what is observed in EcMenD.15 In BsMenD, the side chains of Asp457 and Asn484, the main-chain carbonyl of Gly486, a water molecule, and two oxygen atoms from the diphosphate group form an octahedral coordination sphere about the metal ion (Fig. 5).

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