Evolution of enzymatic activities in the enolase superfamily

Galactarate dehydratase III from agrobacterium tumefaciens C58

Fiona P. Groninger-Poe, Jason T. Bouvier, Matthew W. Vetting, Chakrapani Kalyanaraman, Ritesh Kumar, Steven C. Almo, Matthew P. Jacobson, John A. Gerlt

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

The genome of Agrobacterium tumefaciens C58 encodes 12 members of the enolase superfamily (ENS), eight of which are members of the mandelate racemase (MR) subgroup and, therefore, likely to be acid sugar dehydratases. Using a library of 77 acid sugars for high-throughput screening, one protein (UniProt entry A9CG74; locus tag Atu4196) showed activity with both m-galactarate and d-galacturonate. Two families of galactarate dehydratases had been discovered previously in the ENS, GalrD/TalrD [Yew, W. S., et al. (2007) Biochemistry 46, 9564-9577] and GalrD-II [Rakus, J. F., et al. (2009) Biochemistry 48, 11546-11558]; these have different active site acid/base catalysis and have no activity with d-galacturonate. A9CG74 dehydrates m-galactarate to form 2-keto-3-deoxy-galactarate but does not dehydrate d-galacturonate as expected. Instead, when A9CG74 is incubated with d-galacturonate, 3-deoxy-d-xylo-hexarate or 3-deoxy-d-lyxo-hexarate is formed. In this reaction, instead of abstracting the C5 proton α to the carboxylate group, the expected reaction for a member of the ENS, the enzyme apparently abstracts the proton α to the aldehyde group to form 3-deoxy-d-threo-hexulosuronate that undergoes a 1,2-hydride shift similar to the benzylic acid rearrangement to form the observed product. A. tumefaciens C58 does not utilize m-galactarate as a carbon source under the conditions tested in this study, although it does utilize d-galacturonate, which is a likely precursor to m-galactarate. The gene encoding A9CG74 and several genome proximal genes were upregulated with d-galacturonate as the carbon source. One of these, a member of the dihydrodipicolinate synthase superfamily, catalyzes the dehydration and subsequent decarboxylation of 2-keto-3-deoxy-d-galactarate to α-ketoglutarate semialdehyde, thereby providing a pathway for the conversion of m-galactarate to α-ketoglutarate semialdehyde.

Original languageEnglish (US)
Pages (from-to)4192-4203
Number of pages12
JournalBiochemistry
Volume53
Issue number25
DOIs
StatePublished - Jul 1 2014

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Hydro-Lyases
Agrobacterium tumefaciens
Phosphopyruvate Hydratase
Sugar Acids
Biochemistry
Genes
mandelate racemase
4-hydroxy-tetrahydrodipicolinate synthase
Protons
Carbon
Genome
Decarboxylation
Gene encoding
Acids
Catalysis
Dehydration
Aldehydes
Hydrides
Catalytic Domain
Screening

ASJC Scopus subject areas

  • Biochemistry

Cite this

Groninger-Poe, F. P., Bouvier, J. T., Vetting, M. W., Kalyanaraman, C., Kumar, R., Almo, S. C., ... Gerlt, J. A. (2014). Evolution of enzymatic activities in the enolase superfamily: Galactarate dehydratase III from agrobacterium tumefaciens C58. Biochemistry, 53(25), 4192-4203. https://doi.org/10.1021/bi5005377

Evolution of enzymatic activities in the enolase superfamily : Galactarate dehydratase III from agrobacterium tumefaciens C58. / Groninger-Poe, Fiona P.; Bouvier, Jason T.; Vetting, Matthew W.; Kalyanaraman, Chakrapani; Kumar, Ritesh; Almo, Steven C.; Jacobson, Matthew P.; Gerlt, John A.

In: Biochemistry, Vol. 53, No. 25, 01.07.2014, p. 4192-4203.

Research output: Contribution to journalArticle

Groninger-Poe, FP, Bouvier, JT, Vetting, MW, Kalyanaraman, C, Kumar, R, Almo, SC, Jacobson, MP & Gerlt, JA 2014, 'Evolution of enzymatic activities in the enolase superfamily: Galactarate dehydratase III from agrobacterium tumefaciens C58', Biochemistry, vol. 53, no. 25, pp. 4192-4203. https://doi.org/10.1021/bi5005377
Groninger-Poe, Fiona P. ; Bouvier, Jason T. ; Vetting, Matthew W. ; Kalyanaraman, Chakrapani ; Kumar, Ritesh ; Almo, Steven C. ; Jacobson, Matthew P. ; Gerlt, John A. / Evolution of enzymatic activities in the enolase superfamily : Galactarate dehydratase III from agrobacterium tumefaciens C58. In: Biochemistry. 2014 ; Vol. 53, No. 25. pp. 4192-4203.
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