5OYN

Crystal structure of D-xylonate dehydratase in holo-form

Summary for 5OYN

• Entry DOI: 10.2210/pdb5oyn/pdb
• Descriptor: Dehydratase, IlvD/Edd family, MAGNESIUM ION, FE2/S2 (INORGANIC) CLUSTER, ... (4 entities in total)
• Functional Keywords: d-xylonate dehydratase, ilvd/edd enzyme, [2fe-2s] cluster, pentonate dehydratase, hydrolyase, lyase
• Biological source: Caulobacter crescentus (strain ATCC 19089 / CB15)
• Total number of polymer chains: 4
• Total formula weight: 262696.58

Authors

Rahman, M.M.,Rouvinen, J.,Hakulinen, N. (deposition date: 2017-09-11, release date: 2018-01-24, Last modification date: 2018-04-18)

Primary citation

Rahman, M.M.,Andberg, M.,Koivula, A.,Rouvinen, J.,Hakulinen, N.
The crystal structure of D-xylonate dehydratase reveals functional features of enzymes from the Ilv/ED dehydratase family.
Sci Rep, 8:865-865, 2018

PubMed Abstract: 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 Mg 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.

PubMed: 29339766
DOI: 10.1038/s41598-018-19192-6

Experimental method

X-RAY DIFFRACTION (2.7 Å)