The Crystal Structure of a Bacterial l -Arabinonate Dehydratase Contains a [2Fe-2S] Cluster

Mohammad Rahman, Martina Andberg, Senthil Thangaraj, Tarja Parkkinen, Merja Penttilä, Janne Jänis, Anu Koivula, Juha Rouvinen, Nina Hakulinen (Corresponding Author)

Research output: Contribution to journal › Article › Scientific › peer-review

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Abstract

We present a novel crystal structure of the IlvD/EDD family enzyme, l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT, EC 4.2.1.25), which catalyzes the conversion of l-arabinonate to 2-dehydro-3-deoxy-L-arabinonate. The enzyme is a tetramer consisting of a dimer of dimers, where each monomer is composed of two domains. The active site contains a catalytically important [2Fe-2S] cluster and Mg2+ ion and is buried between two domains, and also at the dimer interface. The active site Lys129 was found to be carbamylated. Ser480 and Thr482 were shown to be essential residues for catalysis, and the S480A mutant structure showed an unexpected open conformation in which the active site was more accessible for the substrate. This structure showed the partial binding of L-arabinonate, which allowed us to suggest that the alkoxide ion form of the Ser480 side chain functions as a base and the [2Fe-2S] cluster functions as a Lewis acid in the elimination reaction.
Original languageEnglish
Pages (from-to)1919-1927
Number of pages9
JournalACS Chemical Biology
Volume12
Issue number7
DOIs
Publication statusPublished - 21 Jul 2017
MoE publication typeA1 Journal article-refereed

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Hydro-Lyases
Bacterial Structures
Dimers
Catalytic Domain
Crystal structure
Rhizobium leguminosarum
Ions
Lewis Acids
Enzymes
Catalysis
Conformations
Monomers
Substrates

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Rahman, Mohammad ; Andberg, Martina ; Thangaraj, Senthil ; Parkkinen, Tarja ; Penttilä, Merja ; Jänis, Janne ; Koivula, Anu ; Rouvinen, Juha ; Hakulinen, Nina. / The Crystal Structure of a Bacterial l -Arabinonate Dehydratase Contains a [2Fe-2S] Cluster. In: ACS Chemical Biology. 2017 ; Vol. 12, No. 7. pp. 1919-1927.
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abstract = "We present a novel crystal structure of the IlvD/EDD family enzyme, l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT, EC 4.2.1.25), which catalyzes the conversion of l-arabinonate to 2-dehydro-3-deoxy-L-arabinonate. The enzyme is a tetramer consisting of a dimer of dimers, where each monomer is composed of two domains. The active site contains a catalytically important [2Fe-2S] cluster and Mg2+ ion and is buried between two domains, and also at the dimer interface. The active site Lys129 was found to be carbamylated. Ser480 and Thr482 were shown to be essential residues for catalysis, and the S480A mutant structure showed an unexpected open conformation in which the active site was more accessible for the substrate. This structure showed the partial binding of L-arabinonate, which allowed us to suggest that the alkoxide ion form of the Ser480 side chain functions as a base and the [2Fe-2S] cluster functions as a Lewis acid in the elimination reaction.",
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Rahman, M, Andberg, M, Thangaraj, S, Parkkinen, T, Penttilä, M, Jänis, J, Koivula, A, Rouvinen, J & Hakulinen, N 2017, 'The Crystal Structure of a Bacterial l -Arabinonate Dehydratase Contains a [2Fe-2S] Cluster', ACS Chemical Biology, vol. 12, no. 7, pp. 1919-1927. https://doi.org/10.1021/acschembio.7b00304

The Crystal Structure of a Bacterial l -Arabinonate Dehydratase Contains a [2Fe-2S] Cluster. / Rahman, Mohammad; Andberg, Martina; Thangaraj, Senthil; Parkkinen, Tarja; Penttilä, Merja; Jänis, Janne; Koivula, Anu; Rouvinen, Juha; Hakulinen, Nina (Corresponding Author).

In: ACS Chemical Biology, Vol. 12, No. 7, 21.07.2017, p. 1919-1927.

Research output: Contribution to journal › Article › Scientific › peer-review

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T1 - The Crystal Structure of a Bacterial l -Arabinonate Dehydratase Contains a [2Fe-2S] Cluster

AU - Rahman, Mohammad

AU - Andberg, Martina

AU - Thangaraj, Senthil

AU - Parkkinen, Tarja

AU - Penttilä, Merja

AU - Jänis, Janne

AU - Koivula, Anu

AU - Rouvinen, Juha

AU - Hakulinen, Nina

PY - 2017/7/21

Y1 - 2017/7/21

N2 - We present a novel crystal structure of the IlvD/EDD family enzyme, l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT, EC 4.2.1.25), which catalyzes the conversion of l-arabinonate to 2-dehydro-3-deoxy-L-arabinonate. The enzyme is a tetramer consisting of a dimer of dimers, where each monomer is composed of two domains. The active site contains a catalytically important [2Fe-2S] cluster and Mg2+ ion and is buried between two domains, and also at the dimer interface. The active site Lys129 was found to be carbamylated. Ser480 and Thr482 were shown to be essential residues for catalysis, and the S480A mutant structure showed an unexpected open conformation in which the active site was more accessible for the substrate. This structure showed the partial binding of L-arabinonate, which allowed us to suggest that the alkoxide ion form of the Ser480 side chain functions as a base and the [2Fe-2S] cluster functions as a Lewis acid in the elimination reaction.

AB - We present a novel crystal structure of the IlvD/EDD family enzyme, l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT, EC 4.2.1.25), which catalyzes the conversion of l-arabinonate to 2-dehydro-3-deoxy-L-arabinonate. The enzyme is a tetramer consisting of a dimer of dimers, where each monomer is composed of two domains. The active site contains a catalytically important [2Fe-2S] cluster and Mg2+ ion and is buried between two domains, and also at the dimer interface. The active site Lys129 was found to be carbamylated. Ser480 and Thr482 were shown to be essential residues for catalysis, and the S480A mutant structure showed an unexpected open conformation in which the active site was more accessible for the substrate. This structure showed the partial binding of L-arabinonate, which allowed us to suggest that the alkoxide ion form of the Ser480 side chain functions as a base and the [2Fe-2S] cluster functions as a Lewis acid in the elimination reaction.

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DO - 10.1021/acschembio.7b00304

M3 - Article

VL - 12

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JO - ACS Chemical Biology

JF - ACS Chemical Biology

SN - 1554-8929

IS - 7

ER -

Rahman M, Andberg M, Thangaraj S, Parkkinen T, Penttilä M, Jänis J et al. The Crystal Structure of a Bacterial l -Arabinonate Dehydratase Contains a [2Fe-2S] Cluster. ACS Chemical Biology. 2017 Jul 21;12(7):1919-1927. https://doi.org/10.1021/acschembio.7b00304

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