4ZAV

UbiX in complex with a covalent adduct between dimethylallyl monophosphate and reduced FMN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.129 
  • R-Value Work: 0.098 
  • R-Value Observed: 0.099 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis.

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

(2015) Nature 522: 497-501

  • DOI: 10.1038/nature14559
  • Primary Citation of Related Structures:  
    4ZAF, 4ZAG, 4ZAL, 4ZAN, 4ZAV, 4ZAW, 4ZAX, 4ZAY, 4ZAZ

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UbiXA209Pseudomonas aeruginosaMutation(s): 0 
Gene Names: PA4019
EC: 4.1.1 (PDB Primary Data), 2.5.1.129 (UniProt)
UniProt
Find proteins for Q9HX08 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HX08 
Go to UniProtKB:  Q9HX08
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4LS (Subject of Investigation/LOI)
Query on 4LS

Download Ideal Coordinates CCD File 
B [auth A]1-deoxy-1-[7,8-dimethyl-5-(3-methylbut-2-en-1-yl)-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono -D-ribitol
C22 H31 N4 O9 P
BJBVBUWJZZTUOU-SCTDSRPQSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
SCN
Query on SCN

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.129 
  • R-Value Work: 0.098 
  • R-Value Observed: 0.099 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.18α = 90
b = 142.18β = 90
c = 142.18γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2015-04-14 
  • Released Date: 2015-06-17 
  • Deposition Author(s): White, M.D., Leys, D.

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-07-01
    Changes: Database references