PDBsum entry 4q5o

Oxidoreductase

PDB id: 4q5o

Contents

Protein chains

282 a.a.

Ligands

AKG ×2

6CS ×2

Metals

_FE ×2

Waters ×29

PDB id:

4q5o

Name:

Oxidoreductase

Title:

Crystal structure of ectd from s. Alaskensis with 2-oxoglutarate and 5-hydroxyectoine

Structure:

Ectoine hydroxylase. Chain: a, b. Engineered: yes

Source:

Sphingopyxis alaskensis rb2256. Organism_taxid: 317655. Strain: dsm 13593 / lmg 18877 / rb2256. Gene: sala_2952. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.64Å R-factor: 0.210 R-free: 0.279

Authors:

A.Hoeppner,N.Widderich,E.Bremer,S.H.Smits

Key ref:

A.Höppner et al. (2014). Crystal structure of the ectoine hydroxylase, a snapshot of the active site. J Biol Chem, 289, 29570-29583. PubMed id: 25172507 DOI: 10.1074/jbc.M114.576769

Date:

17-Apr-14 Release date: 10-Sep-14

Protein chains

Q1GNW5  (Q1GNW5_SPHAL) -  Ectoine dioxygenase from Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256)

Seq: 306 a.a.

Struc: 282 a.a.

Enzyme reactions

• Enzyme class: E.C.1.14.11.55 - ectoine hydroxylase.
• Reaction: L-ectoine + 2-oxoglutarate + O2 = 5-hydroxyectoine + succinate + CO2

L-ectoine (Bound ligand (Het Group name = AKG) corresponds exactly) + 2-oxoglutarate + O2 = 5-hydroxyectoine (Bound ligand (Het Group name = 6CS) corresponds exactly) + succinate + CO2

• Cofactor: Ascorbate; Fe(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M114.576769

J Biol Chem 289:29570-29583 (2014)

PubMed id: 25172507

Crystal structure of the ectoine hydroxylase, a snapshot of the active site.

A.Höppner, N.Widderich, M.Lenders, E.Bremer, S.H.Smits.

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.