4Q5O

Crystal structure of EctD from S. alaskensis with 2-oxoglutarate and 5-hydroxyectoine

Summary for 4Q5O

• Entry DOI: 10.2210/pdb4q5o/pdb
• Related: 4MHR 4MHU 4NMI
• Descriptor: Ectoine hydroxylase, FE (III) ION, 2-OXOGLUTARIC ACID, ... (5 entities in total)
• Functional Keywords: jelly-roll or cupin fold, ectoine hydroxylase, oxidoreductase
• Biological source: Sphingopyxis alaskensis RB2256
• Total number of polymer chains: 2
• Total formula weight: 71173.40

Authors

Hoeppner, A.,Widderich, N.,Bremer, E.,Smits, S.H. (deposition date: 2014-04-17, release date: 2014-09-10, Last modification date: 2023-09-20)

Primary citation

Hoppner, A.,Widderich, N.,Lenders, M.,Bremer, E.,Smits, S.H.
Crystal structure of the ectoine hydroxylase, a snapshot of the active site.
J.Biol.Chem., 289:29570-29583, 2014

PubMed Abstract: Ectoine and its derivative 5-hydroxyectoine are compatible solutes that are widely synthesized by bacteria to cope physiologically with osmotic stress. They also serve as chemical chaperones and maintain the functionality of macromolecules. 5-Hydroxyectoine is produced from ectoine through a stereo-specific hydroxylation, an enzymatic reaction catalyzed by the ectoine hydroxylase (EctD). The EctD protein is a member of the non-heme-containing iron(II) and 2-oxoglutarate-dependent dioxygenase superfamily and is evolutionarily well conserved. We studied the ectoine hydroxylase from the cold-adapted marine ultra-microbacterium Sphingopyxis alaskensis (Sa) and found that the purified SaEctD protein is a homodimer in solution. We determined the SaEctD crystal structure in its apo-form, complexed with the iron catalyst, and in a form that contained iron, the co-substrate 2-oxoglutarate, and the reaction product of EctD, 5-hydroxyectoine. The iron and 2-oxoglutarate ligands are bound within the EctD active site in a fashion similar to that found in other members of the dioxygenase superfamily. 5-Hydroxyectoine, however, is coordinated by EctD in manner different from that found in high affinity solute receptor proteins operating in conjunction with microbial import systems for ectoines. Our crystallographic analysis provides a detailed view into the active site of the ectoine hydroxylase and exposes an intricate network of interactions between the enzyme and its ligands that collectively ensure the hydroxylation of the ectoine substrate in a position- and stereo-specific manner.

PubMed: 25172507
DOI: 10.1074/jbc.M114.576769

Experimental method

X-RAY DIFFRACTION (2.64 Å)