6QLG

Crystal structure of AnUbiX (PadA1) in complex with FMN and dimethylallyl pyrophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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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: https://doi.org/10.1038/s41467-019-10220-1
  • Primary Citation of Related Structures:  
    6QLG, 6QLH, 6QLI, 6QLJ, 6QLK, 6QLL, 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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flavin prenyltransferase PAD1, mitochondrial227Aspergillus nigerMutation(s): 0 
Gene Names: PAD1An03g06570
EC: 2.5.1.129
UniProt
Find proteins for A3F715 (Aspergillus niger)
Explore A3F715 
Go to UniProtKB:  A3F715
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3F715
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
H [auth C]
I [auth C]
M [auth A]
Q [auth D]
S [auth E]
H [auth C],
I [auth C],
M [auth A],
Q [auth D],
S [auth E],
T [auth F]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
DMA
Query on DMA

Download Ideal Coordinates CCD File 
G [auth C]
J [auth C]
N [auth B]
O [auth B]
P [auth D]
G [auth C],
J [auth C],
N [auth B],
O [auth B],
P [auth D],
U [auth F]
DIMETHYLALLYL DIPHOSPHATE
C5 H12 O7 P2
CBIDRCWHNCKSTO-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
L [auth A],
R [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
K [auth C]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102α = 90
b = 102β = 90
c = 276.69γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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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: 2024-05-15
    Changes: Data collection, Database references