Evolution of enzymatic activities in the enolase superfamily

L-fuconate dehydratase from Xanthomonas campestris

Wen Shan Yew, Alexander A. Fedorov, Elena V. Fedorov, John F. Rakus, Richard W. Pierce, Steven C. Almo, John A. Gerlt

Research output: Contribution to journalArticle

56 Citations (Scopus)

Abstract

Many members of the mechanistically diverse enolase superfamily have unknown functions. In this report we use both genome (operon) context and screening of a library of acid sugars to assign the L-fuconate dehydratase (FucD) function to a member of the mandelate racemase (MR) subgroup of the superfamily encoded by the Xanthomonas campestris pv. campestris str. ATCC 33913 genome (GI:21233491). Orthologues of FucD are found in both bacteria and eukaryotes, the latter including the rTS beta protein in Homo sapiens that has been implicated in regulating thymidylate synthase activity. As suggested by sequence alignments and confirmed by high-resolution structures in the presence of active site ligands, FucD and MR share the same active site motif of functional groups: three carboxylate ligands for the essential Mg2+ located at the ends of the third, fourth, and fifth β-strands in the (β/α)7β-barrel domain (Asp 248, Glu 274, and Glu 301, respectively), a Lys-x-Lys motif at the end of the second β-strand (Lys 218 and Lys 220), a His-Asp dyad at the end of the seventh and sixth β-strands (His 351 and Asp 324, respectively), and a Glu at the end of the eighth β-strand (Glu 382). The mechanism of the FucD reaction involves initial abstraction of the 2-proton by Lys 220, acid catalysis of the vinylogous β-elimination of the 3-OH group by His 351, and stereospecific ketonization of the resulting enol, likely by the conjugate acid of Lys 220, to yield the 2-keto-3-deoxy-L-fuconate product. Screening of the library of acid sugars revealed substrate and functional promiscuity: In addition to L-fuconate, FucD also catalyzes the dehydration of L-galactonate, D-arabinonate, D-altronate, L-talonate, and D-ribonate. The dehydrations of L-fuconate, L-galactonate, and D-arabinonate are initiated by abstraction of the 2-protons by Lys 220. The dehydrations of L-talonate and D-ribonate are initiated by abstraction of the 2-protons by His 351; however, protonation of the enediolate intermediates by the conjugate acid of Lys 220 yields L-galactonate and D-arabinonate in competition with dehydration. The functional promiscuity discovered for FucD highlights possible structural mechanisms for evolution of function in the enolase superfamily.

Original languageEnglish (US)
Pages (from-to)14582-14597
Number of pages16
JournalBiochemistry
Volume45
Issue number49
DOIs
StatePublished - Dec 12 2006

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Xanthomonas campestris
Phosphopyruvate Hydratase
mandelate racemase
Dehydration
Protons
Sugar Acids
Acids
Catalytic Domain
Screening
Genes
Genome
Ligands
Thymidylate Synthase
Sequence Alignment
Protonation
Operon
Eukaryota
Catalysis
Functional groups
L-fuconate dehydratase

ASJC Scopus subject areas

  • Biochemistry

Cite this

Yew, W. S., Fedorov, A. A., Fedorov, E. V., Rakus, J. F., Pierce, R. W., Almo, S. C., & Gerlt, J. A. (2006). Evolution of enzymatic activities in the enolase superfamily: L-fuconate dehydratase from Xanthomonas campestris. Biochemistry, 45(49), 14582-14597. https://doi.org/10.1021/bi061687o

Evolution of enzymatic activities in the enolase superfamily : L-fuconate dehydratase from Xanthomonas campestris. / Yew, Wen Shan; Fedorov, Alexander A.; Fedorov, Elena V.; Rakus, John F.; Pierce, Richard W.; Almo, Steven C.; Gerlt, John A.

In: Biochemistry, Vol. 45, No. 49, 12.12.2006, p. 14582-14597.

Research output: Contribution to journalArticle

Yew, WS, Fedorov, AA, Fedorov, EV, Rakus, JF, Pierce, RW, Almo, SC & Gerlt, JA 2006, 'Evolution of enzymatic activities in the enolase superfamily: L-fuconate dehydratase from Xanthomonas campestris', Biochemistry, vol. 45, no. 49, pp. 14582-14597. https://doi.org/10.1021/bi061687o
Yew, Wen Shan ; Fedorov, Alexander A. ; Fedorov, Elena V. ; Rakus, John F. ; Pierce, Richard W. ; Almo, Steven C. ; Gerlt, John A. / Evolution of enzymatic activities in the enolase superfamily : L-fuconate dehydratase from Xanthomonas campestris. In: Biochemistry. 2006 ; Vol. 45, No. 49. pp. 14582-14597.
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N2 - Many members of the mechanistically diverse enolase superfamily have unknown functions. In this report we use both genome (operon) context and screening of a library of acid sugars to assign the L-fuconate dehydratase (FucD) function to a member of the mandelate racemase (MR) subgroup of the superfamily encoded by the Xanthomonas campestris pv. campestris str. ATCC 33913 genome (GI:21233491). Orthologues of FucD are found in both bacteria and eukaryotes, the latter including the rTS beta protein in Homo sapiens that has been implicated in regulating thymidylate synthase activity. As suggested by sequence alignments and confirmed by high-resolution structures in the presence of active site ligands, FucD and MR share the same active site motif of functional groups: three carboxylate ligands for the essential Mg2+ located at the ends of the third, fourth, and fifth β-strands in the (β/α)7β-barrel domain (Asp 248, Glu 274, and Glu 301, respectively), a Lys-x-Lys motif at the end of the second β-strand (Lys 218 and Lys 220), a His-Asp dyad at the end of the seventh and sixth β-strands (His 351 and Asp 324, respectively), and a Glu at the end of the eighth β-strand (Glu 382). The mechanism of the FucD reaction involves initial abstraction of the 2-proton by Lys 220, acid catalysis of the vinylogous β-elimination of the 3-OH group by His 351, and stereospecific ketonization of the resulting enol, likely by the conjugate acid of Lys 220, to yield the 2-keto-3-deoxy-L-fuconate product. Screening of the library of acid sugars revealed substrate and functional promiscuity: In addition to L-fuconate, FucD also catalyzes the dehydration of L-galactonate, D-arabinonate, D-altronate, L-talonate, and D-ribonate. The dehydrations of L-fuconate, L-galactonate, and D-arabinonate are initiated by abstraction of the 2-protons by Lys 220. The dehydrations of L-talonate and D-ribonate are initiated by abstraction of the 2-protons by His 351; however, protonation of the enediolate intermediates by the conjugate acid of Lys 220 yields L-galactonate and D-arabinonate in competition with dehydration. The functional promiscuity discovered for FucD highlights possible structural mechanisms for evolution of function in the enolase superfamily.

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