The crystal structure of D-xylonate dehydratase reveals functional features of enzymes from the Ilv/ED dehydratase family

Mohammad Mubinur Rahman, Martina Andberg, Anu Koivula, Juha Rouvinen, Nina Hakulinen

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    17 Citations (Scopus)


    The Ilv/ED dehydratase protein family includes dihydroxy acid-, gluconate-, 6-phosphogluconate- and pentonate dehydratases. The members of this family are involved in various biosynthetic and carbohydrate metabolic pathways. Here, we describe the first crystal structure of D-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) at 2.7 Å resolution and compare it with other available enzyme structures from the IlvD/EDD protein family. The quaternary structure of CcXyDHT is a tetramer, and each monomer is composed of two domains in which the N-terminal domain forms a binding site for a [2Fe-2S] cluster and a Mg2+ ion. The active site is located at the monomer-monomer interface and contains residues from both the N-terminal recognition helix and the C-terminus of the dimeric counterpart. The active site also contains a conserved Ser490, which probably acts as a base in catalysis. Importantly, the cysteines that participate in the binding and formation of the [2Fe-2S] cluster are not all conserved within the Ilv/ED dehydratase family, which suggests that some members of the IlvD/EDD family may bind different types of [Fe-S] clusters.

    Original languageEnglish
    Article number865
    JournalScientific Reports
    Issue number1
    Publication statusPublished - 16 Jan 2018
    MoE publication typeA1 Journal article-refereed


    At UEF, this work received financial support from the Academy of Finland (Decisions 256937 and 292705). The work was part of the Finnish Centre of Excellence in the White Biotechnology-Green Chemistry programme (Academy of Finland Decision 118573) and the IV4SP project (Academy of Finland Decision 272598) at VTT. The work also received funding from the European Community’s Seventh Framework Programme (FP7/2007–2013) under BioStruct-X (Grant Agreement N° 283570).


    • Enzymes
    • X-ray crystallography


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