New superfamily members identified for Schiff-Base enzymes based on verification of catalytically essential residues

Kyung Choi, Vicky Lai, Christine E. Foster, Aaron J. Morris, Dean R. Tolan, Karen N. Allen

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Enzymes that utilize a Schiff-base intermediate formed with their substrates and that share the same α/β barrel fold comprise a mechanistically diverse superfamily defined in the SCOPS database as the class I aldolase family. The family includes the "classical" aldolases fructose-1,6-(bis)phosphate (FBP) aldolase, transaldolase, and 2-keto-3-deoxy-6-phosphogluconate aldolase. Moreover, the N-acetylneuraminate lyase family has been included in the class I aldolase family on the basis of similar Schiff-base chemistry and fold. Herein, we generate primary sequence identities based on structural alignment that support the homology and reveal additional mechanistic similarities beyond the common use of a lysine for Schiff-base formation. The structural and mechanistic correspondence comprises the use of a catalytic dyad, wherein a general acid/base residue (Glu, Tyr, or His) involved in Schiff-base chemistry is stationed on β-strand 5 of the α/β barrel. The role of the acid/base residue was probed by site-directed mutagenesis and steady-state and pre-steady-state kinetics on a representative member of this family, FBP aldolase. The kinetic results are consistent with the participation of this conserved residue or position in the protonation of the carbinolamine intermediate and dehydration of the Schiff base in FBP aldolase and, by analogy, the class I aldolase family.

Original languageEnglish (US)
Pages (from-to)8546-8555
Number of pages10
JournalBiochemistry
Volume45
Issue number28
DOIs
StatePublished - Jul 18 2006
Externally publishedYes

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Fructose-Bisphosphate Aldolase
Schiff Bases
Enzymes
phospho-2-keto-3-deoxy-gluconate aldolase
N-acetylneuraminate lyase
Transaldolase
Aldehyde-Lyases
Mutagenesis
Kinetics
Acids
Protonation
Site-Directed Mutagenesis
Fructose
Dehydration
Lysine
Phosphates
Databases
Substrates

ASJC Scopus subject areas

  • Biochemistry

Cite this

New superfamily members identified for Schiff-Base enzymes based on verification of catalytically essential residues. / Choi, Kyung; Lai, Vicky; Foster, Christine E.; Morris, Aaron J.; Tolan, Dean R.; Allen, Karen N.

In: Biochemistry, Vol. 45, No. 28, 18.07.2006, p. 8546-8555.

Research output: Contribution to journalArticle

Choi, Kyung ; Lai, Vicky ; Foster, Christine E. ; Morris, Aaron J. ; Tolan, Dean R. ; Allen, Karen N. / New superfamily members identified for Schiff-Base enzymes based on verification of catalytically essential residues. In: Biochemistry. 2006 ; Vol. 45, No. 28. pp. 8546-8555.
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