6QLV

Crystal structure of W200H UbiX in complex with a geranyl-FMN N5 adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry.

Marshall, S.A.Payne, K.A.P.Fisher, K.White, M.D.Ni Cheallaigh, A.Balaikaite, A.Rigby, S.E.J.Leys, D.

(2019) Nat Commun 10: 2357-2357

  • DOI: 10.1038/s41467-019-10220-1
  • Primary Citation of Related Structures:  
    6QLJ, 6QLI, 6QLL, 6QLK, 6QLH, 6QLG, 6QLV

  • PubMed Abstract: 
  • The UbiX-UbiD enzymes are widespread in microbes, acting in concert to decarboxylate alpha-beta unsaturated carboxylic acids using a highly modified flavin cofactor, prenylated FMN (prFMN). UbiX serves as the flavin prenyltransferase, extending the isoalloxazine ring system with a fourth non-aromatic ring, derived from sequential linkage between a dimethylallyl moiety and the FMN N5 and C6 ...

    The UbiX-UbiD enzymes are widespread in microbes, acting in concert to decarboxylate alpha-beta unsaturated carboxylic acids using a highly modified flavin cofactor, prenylated FMN (prFMN). UbiX serves as the flavin prenyltransferase, extending the isoalloxazine ring system with a fourth non-aromatic ring, derived from sequential linkage between a dimethylallyl moiety and the FMN N5 and C6. Using structure determination and solution studies of both dimethylallyl monophosphate (DMAP) and dimethyallyl pyrophosphate (DMAPP) dependent UbiX enzymes, we reveal the first step, N5-C1' bond formation, is contingent on the presence of a dimethylallyl substrate moiety. Hence, an S N 1 mechanism similar to other prenyltransferases is proposed. Selected variants of the (pyro)phosphate binding site are unable to catalyse subsequent Friedel-Crafts alkylation of the flavin C6, but can be rescued by addition of (pyro)phosphate. Thus, retention of the (pyro)phosphate leaving group is required for C6-C3' bond formation, resembling pyrophosphate initiated class I terpene cyclase reaction chemistry.


    Organizational Affiliation

    Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK. david.leys@manchester.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Flavin prenyltransferase UbiX
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
230Pseudomonas aeruginosaMutation(s): 1 
Gene Names: 
EC: 2.5.1.129
UniProt
Find proteins for A0A072ZCW8 (Pseudomonas aeruginosa)
Explore A0A072ZCW8 
Go to UniProtKB:  A0A072ZCW8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HJN (Subject of Investigation/LOI)
Query on HJN

Download Ideal Coordinates CCD File 
HA [auth G], PA [auth I], U [auth C][(2~{R},3~{S},4~{S})-5-[5-[(2~{Z})-3,7-dimethylocta-2,6-dienyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate
C27 H39 N4 O9 P
NUMSCVAFXSDOGX-QKMBGELKSA-N
 Ligand Interaction
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
BA [auth F] , JA [auth H] , N [auth A] , O [auth B] , QA [auth J] , VA [auth K] , WA [auth L] , X [auth D] , 
BA [auth F],  JA [auth H],  N [auth A],  O [auth B],  QA [auth J],  VA [auth K],  WA [auth L],  X [auth D],  Z [auth E]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
HZZ (Subject of Investigation/LOI)
Query on HZZ

Download Ideal Coordinates CCD File 
FA [auth G] , KA [auth H] , M [auth A] , NA [auth I] , Q [auth B] , S [auth C] , SA [auth J] , UA [auth K] , 
FA [auth G],  KA [auth H],  M [auth A],  NA [auth I],  Q [auth B],  S [auth C],  SA [auth J],  UA [auth K],  XA [auth L]
[(2~{Z})-3,7-dimethylocta-2,6-dienyl] dihydrogen phosphate
C10 H19 O4 P
FFOWJDCTFSWUMJ-YFHOEESVSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth E], EA [auth F], Y [auth D]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
CA [auth F], GA [auth G], LA [auth H], OA [auth I], P [auth B], RA [auth J], T [auth C]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
DA [auth F], IA [auth G], MA [auth I], R [auth B], TA [auth J], V [auth C], W [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.533α = 90
b = 164.931β = 90
c = 102.527γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K017802/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P000622/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-21
    Changes: Data collection