Structure and function of a decarboxylating Agrobacterium tumefaciens Keto-deoxy-D-galactarate dehydratase

Helena Taberman, Martina Andberg, Tarja Parkkinen, Janne Jänis, Merja Penttilä, Nina Hakulinen, Anu Koivula, Juha Rouvinen (Corresponding Author)

Research output: Contribution to journalArticleScientificpeer-review

7 Citations (Scopus)

Abstract

(Figure Presented) Agrobacterium tumefaciens (At) strain C58 contains an oxidative enzyme pathway that can function on both D-glucuronic and D-galacturonic acid. The corresponding gene coding for At keto-deoxy-D-galactarate (KDG) dehydratase is located in the same gene cluster as those coding for uronate dehydrogenase (At Udh) and galactarolactone cycloisomerase (At Gci) which we have previously characterized. Here, we present the kinetic characterization and crystal structure of At KDG dehydratase, which catalyzes the next step, the decarboxylating hydrolyase reaction of KDG to produce α-ketoglutaric semialdehyde (α-KGSA) and carbon dioxide. The crystal structures of At KDG dehydratase and its complexes with pyruvate and 2-oxoadipic acid, two substrate analogues, were determined to 1.7 A˚, 1.5 A˚, and 2.1 A˚ resolution, respectively. Furthermore, mass spectrometry was used to confirm reaction end-products. The results lead us to propose a structure-based mechanism for At KDG dehydratase, suggesting that while the enzyme belongs to the Class I aldolase protein family, it does not follow a typical retro-aldol condensation mechanism.

Original languageEnglish
Pages (from-to)8052-8060
Number of pages9
JournalBiochemistry
Volume53
Issue number51
DOIs
Publication statusPublished - 30 Dec 2014
MoE publication typeA1 Journal article-refereed

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Hydro-Lyases
Agrobacterium tumefaciens
uronate dehydrogenase
Genes
Crystal structure
Fructose-Bisphosphate Aldolase
Enzymes
Pyruvic Acid
Carbon Dioxide
Mass spectrometry
Condensation
Multigene Family
Mass Spectrometry
Kinetics
Substrates
Proteins

Cite this

Taberman, Helena ; Andberg, Martina ; Parkkinen, Tarja ; Jänis, Janne ; Penttilä, Merja ; Hakulinen, Nina ; Koivula, Anu ; Rouvinen, Juha. / Structure and function of a decarboxylating Agrobacterium tumefaciens Keto-deoxy-D-galactarate dehydratase. In: Biochemistry. 2014 ; Vol. 53, No. 51. pp. 8052-8060.
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abstract = "(Figure Presented) Agrobacterium tumefaciens (At) strain C58 contains an oxidative enzyme pathway that can function on both D-glucuronic and D-galacturonic acid. The corresponding gene coding for At keto-deoxy-D-galactarate (KDG) dehydratase is located in the same gene cluster as those coding for uronate dehydrogenase (At Udh) and galactarolactone cycloisomerase (At Gci) which we have previously characterized. Here, we present the kinetic characterization and crystal structure of At KDG dehydratase, which catalyzes the next step, the decarboxylating hydrolyase reaction of KDG to produce α-ketoglutaric semialdehyde (α-KGSA) and carbon dioxide. The crystal structures of At KDG dehydratase and its complexes with pyruvate and 2-oxoadipic acid, two substrate analogues, were determined to 1.7 A˚, 1.5 A˚, and 2.1 A˚ resolution, respectively. Furthermore, mass spectrometry was used to confirm reaction end-products. The results lead us to propose a structure-based mechanism for At KDG dehydratase, suggesting that while the enzyme belongs to the Class I aldolase protein family, it does not follow a typical retro-aldol condensation mechanism.",
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Structure and function of a decarboxylating Agrobacterium tumefaciens Keto-deoxy-D-galactarate dehydratase. / Taberman, Helena; Andberg, Martina; Parkkinen, Tarja; Jänis, Janne; Penttilä, Merja; Hakulinen, Nina; Koivula, Anu; Rouvinen, Juha (Corresponding Author).

In: Biochemistry, Vol. 53, No. 51, 30.12.2014, p. 8052-8060.

Research output: Contribution to journalArticleScientificpeer-review

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T1 - Structure and function of a decarboxylating Agrobacterium tumefaciens Keto-deoxy-D-galactarate dehydratase

AU - Taberman, Helena

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AU - Penttilä, Merja

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AU - Koivula, Anu

AU - Rouvinen, Juha

PY - 2014/12/30

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N2 - (Figure Presented) Agrobacterium tumefaciens (At) strain C58 contains an oxidative enzyme pathway that can function on both D-glucuronic and D-galacturonic acid. The corresponding gene coding for At keto-deoxy-D-galactarate (KDG) dehydratase is located in the same gene cluster as those coding for uronate dehydrogenase (At Udh) and galactarolactone cycloisomerase (At Gci) which we have previously characterized. Here, we present the kinetic characterization and crystal structure of At KDG dehydratase, which catalyzes the next step, the decarboxylating hydrolyase reaction of KDG to produce α-ketoglutaric semialdehyde (α-KGSA) and carbon dioxide. The crystal structures of At KDG dehydratase and its complexes with pyruvate and 2-oxoadipic acid, two substrate analogues, were determined to 1.7 A˚, 1.5 A˚, and 2.1 A˚ resolution, respectively. Furthermore, mass spectrometry was used to confirm reaction end-products. The results lead us to propose a structure-based mechanism for At KDG dehydratase, suggesting that while the enzyme belongs to the Class I aldolase protein family, it does not follow a typical retro-aldol condensation mechanism.

AB - (Figure Presented) Agrobacterium tumefaciens (At) strain C58 contains an oxidative enzyme pathway that can function on both D-glucuronic and D-galacturonic acid. The corresponding gene coding for At keto-deoxy-D-galactarate (KDG) dehydratase is located in the same gene cluster as those coding for uronate dehydrogenase (At Udh) and galactarolactone cycloisomerase (At Gci) which we have previously characterized. Here, we present the kinetic characterization and crystal structure of At KDG dehydratase, which catalyzes the next step, the decarboxylating hydrolyase reaction of KDG to produce α-ketoglutaric semialdehyde (α-KGSA) and carbon dioxide. The crystal structures of At KDG dehydratase and its complexes with pyruvate and 2-oxoadipic acid, two substrate analogues, were determined to 1.7 A˚, 1.5 A˚, and 2.1 A˚ resolution, respectively. Furthermore, mass spectrometry was used to confirm reaction end-products. The results lead us to propose a structure-based mechanism for At KDG dehydratase, suggesting that while the enzyme belongs to the Class I aldolase protein family, it does not follow a typical retro-aldol condensation mechanism.

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