PDBsum entry 4zaw

Lyase

PDB id: 4zaw

Contents

Protein chain

207 a.a.

Ligands

4LU

SCN

PO4 ×2

Waters ×100

PDB id:

4zaw

Name:

Lyase

Title:

Structure of ubix in complex with reduced prenylated fmn

Structure:

Probable aromatic acid decarboxylase. Chain: a. Engineered: yes

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Gene: pa4019. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.89Å R-factor: 0.150 R-free: 0.192

Authors:

M.D.White,D.Leys

Key ref:

M.D.White et al. (2015). UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis. Nature, 522, 502-506. PubMed id: 26083743 DOI: 10.1038/nature14559

Date:

14-Apr-15 Release date: 17-Jun-15

Protein chain

Q9HX08  (UBIX_PSEAE) -  Flavin prenyltransferase UbiX from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 209 a.a.

Struc: 207 a.a.

Enzyme reactions

• Enzyme class: E.C.2.5.1.129 - flavin prenyltransferase.
• Reaction: dimethylallyl phosphate + FMNH2 = prenylated FMNH2 + phosphate

dimethylallyl phosphate + FMNH2 (Bound ligand (Het Group name = 4LU) matches with 86.11% similarity) = prenylated FMNH2 (Bound ligand (Het Group name = PO4) corresponds exactly) + phosphate

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

Added reference

DOI no: 10.1038/nature14559

Nature 522:502-506 (2015)

PubMed id: 26083743

UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis.

M.D.White, K.A.Payne, K.Fisher, S.A.Marshall, D.Parker, N.J.Rattray, D.K.Trivedi, R.Goodacre, S.E.Rigby, N.S.Scrutton, S.Hay, D.Leys.

ABSTRACT

Ubiquinone (also known as coenzyme Q) is a ubiquitous lipid-soluble redox cofactor that is an essential component of electron transfer chains. Eleven genes have been implicated in bacterial ubiquinone biosynthesis, including ubiX and ubiD, which are responsible for decarboxylation of the 3-octaprenyl-4-hydroxybenzoate precursor. Despite structural and biochemical characterization of UbiX as a flavin mononucleotide (FMN)-binding protein, no decarboxylase activity has been detected. Here we report that UbiX produces a novel flavin-derived cofactor required for the decarboxylase activity of UbiD. UbiX acts as a flavin prenyltransferase, linking a dimethylallyl moiety to the flavin N5 and C6 atoms. This adds a fourth non-aromatic ring to the flavin isoalloxazine group. In contrast to other prenyltransferases, UbiX is metal-independent and requires dimethylallyl-monophosphate as substrate. Kinetic crystallography reveals that the prenyltransferase mechanism of UbiX resembles that of the terpene synthases. The active site environment is dominated by π systems, which assist phosphate-C1' bond breakage following FMN reduction, leading to formation of the N5-C1' bond. UbiX then acts as a chaperone for adduct reorientation, via transient carbocation species, leading ultimately to formation of the dimethylallyl C3'-C6 bond. Our findings establish the mechanism for formation of a new flavin-derived cofactor, extending both flavin and terpenoid biochemical repertoires.