Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase suggests emergence of novel substrate specificity in the enolase superfamily

Saeyoung Lee, Kyoung Heon Kim, Hye Yeon Kim, In-Geol Choi

Research output: Contribution to journalArticle

Abstract

3,6-Anydro-L-galatonate cycloisomerase (ACI) catalyzes the cycloisomerization of a 3,6-anhydro-L-galactonic acid known as a novel metabolite in agarolytic bacteria. Here, we present 3-D structures of ACI from Vibrio sp. strain EJY3 (VejACI) in native and mutant forms at 2.2 Å and 2.6 Å resolutions, respectively. The enzyme belongs to the mandelate racemase subgroup of the enolase superfamily catalyzing common β-elimination reactions by α-carbon deprotonation of substrates. The structure of VejACI revealed a notable 20s loop region in the capping domain, which can be a highly conserved structural motif in ACI homologs of agar metabolism. By comparing mutant (mVejAC/H300 N) and native VejACI structures, we identified a conformational change of Ile142 in VejACI that causes spatial expansion in the binding pocket. These observations imply that Ile142 and the 20s loop play important roles in enzymatic reactivity and substrate specificity. The structural phylogenetic analysis of the enolase superfamily including ACIs revealed sequential, structural, and functional relationships related to the emergence of novel substrate specificity.

Original languageEnglish
Pages (from-to)217-222
Number of pages6
JournalBiochemical and Biophysical Research Communications
Volume491
Issue number1
DOIs
Publication statusPublished - 2017 Sep 9

Fingerprint

Phosphopyruvate Hydratase
mandelate racemase
Substrate Specificity
Crystal structure
Vibrio
Substrates
Agar
Deprotonation
Carbon
Metabolites
Bacteria
Metabolism
Structural analysis
Enzymes
galactonic acid

Keywords

  • 20s loop
  • 3,6-Anhydro-L-galactonate
  • 3,6-Anydro-L-galatonate cycloisomerase
  • Agar metabolism
  • Enolase superfamily

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

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title = "Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase suggests emergence of novel substrate specificity in the enolase superfamily",
abstract = "3,6-Anydro-L-galatonate cycloisomerase (ACI) catalyzes the cycloisomerization of a 3,6-anhydro-L-galactonic acid known as a novel metabolite in agarolytic bacteria. Here, we present 3-D structures of ACI from Vibrio sp. strain EJY3 (VejACI) in native and mutant forms at 2.2 {\AA} and 2.6 {\AA} resolutions, respectively. The enzyme belongs to the mandelate racemase subgroup of the enolase superfamily catalyzing common β-elimination reactions by α-carbon deprotonation of substrates. The structure of VejACI revealed a notable 20s loop region in the capping domain, which can be a highly conserved structural motif in ACI homologs of agar metabolism. By comparing mutant (mVejAC/H300 N) and native VejACI structures, we identified a conformational change of Ile142 in VejACI that causes spatial expansion in the binding pocket. These observations imply that Ile142 and the 20s loop play important roles in enzymatic reactivity and substrate specificity. The structural phylogenetic analysis of the enolase superfamily including ACIs revealed sequential, structural, and functional relationships related to the emergence of novel substrate specificity.",
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AU - Choi, In-Geol

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AB - 3,6-Anydro-L-galatonate cycloisomerase (ACI) catalyzes the cycloisomerization of a 3,6-anhydro-L-galactonic acid known as a novel metabolite in agarolytic bacteria. Here, we present 3-D structures of ACI from Vibrio sp. strain EJY3 (VejACI) in native and mutant forms at 2.2 Å and 2.6 Å resolutions, respectively. The enzyme belongs to the mandelate racemase subgroup of the enolase superfamily catalyzing common β-elimination reactions by α-carbon deprotonation of substrates. The structure of VejACI revealed a notable 20s loop region in the capping domain, which can be a highly conserved structural motif in ACI homologs of agar metabolism. By comparing mutant (mVejAC/H300 N) and native VejACI structures, we identified a conformational change of Ile142 in VejACI that causes spatial expansion in the binding pocket. These observations imply that Ile142 and the 20s loop play important roles in enzymatic reactivity and substrate specificity. The structural phylogenetic analysis of the enolase superfamily including ACIs revealed sequential, structural, and functional relationships related to the emergence of novel substrate specificity.

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