5m1c

From Proteopedia

Crystal structure of N-terminally tagged apo-UbiD from E. coli

PDB ID 5m1c

Drag the structure with the mouse to rotate

Structural highlights

5m1c is a 3 chain structure with sequence from Escherichia coli CFT073. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.75Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UBID_ECOL6 Catalyzes the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol, an intermediate step in ubiquinone biosynthesis.

Publication Abstract from PubMed

The activity of the reversible decarboxylase enzyme Fdc1 is dependent on prenylated FMN (prFMN), a recently discovered cofactor. The oxidized prFMN supports a 1,3-dipolar cycloaddition mechanism that underpins reversible decarboxylation. Fdc1 is a distinct member of the UbiD family of enzymes, with the canonical UbiD catalyzing the (de)carboxylation of para-hydroxybenzoic acid-type substrates. Here we show that the Escherichia coli UbiD enzyme, which is implicated in ubiquinone biosynthesis, cannot be isolated in an active holo-enzyme form, despite the fact active holo-Fdc1 is readily obtained. Formation of holo-UbiD requires reconstitution in vitro of the apo-UbiD with reduced prFMN. Furthermore, while the Fdc1 apo-enzyme can be readily reconstituted and activated, in vitro oxidation to the mature prFMN cofactor stalls at formation of a radical prFMN species in holo-UbiD. Further oxidative maturation in vitro occurs only at alkaline pH, suggesting a proton-coupled electron transfer precedes formation of the fully oxidized prFMN. Crystal structures of holo-UbiD reveal a relatively open active site, potentially occluded from solvent through domain motion. The presence of a prFMN sulfite-adduct in one of the UbiD crystal structures confirms oxidative maturation does occur at ambient pH on a slow time scale. Activity could not be detected for a range of putative para-hydroxybenzoic acid substrates tested. However, the lack of an obvious hydrophobic binding pocket for the octaprenyl-tail of the proposed ubiquinone precursor substrate does suggest UbiD might act on a non-prenylated precursor. Our data reveals unexpected variation occurs in domain mobility, prFMN binding and maturation by the UbiD enzyme family.

Oxidative maturation and Structural Characterization of Prenylated-FMN binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis.,Marshall SA, Fisher K, Ni Cheallaigh A, White MD, Payne KA, Parker DA, Rigby SE, Leys D J Biol Chem. 2017 Jan 5. pii: jbc.M116.762732. doi: 10.1074/jbc.M116.762732. PMID:28057757^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Marshall SA, Fisher K, Ni Cheallaigh A, White MD, Payne KA, Parker DA, Rigby SE, Leys D. Oxidative maturation and Structural Characterization of Prenylated-FMN binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis. J Biol Chem. 2017 Jan 5. pii: jbc.M116.762732. doi: 10.1074/jbc.M116.762732. PMID:28057757 doi:http://dx.doi.org/10.1074/jbc.M116.762732