6QLG | pdb_00006qlg

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

PDB DOI: https://doi.org/10.2210/pdb6QLG/pdb

Classification: TRANSFERASE
Organism(s): Aspergillus niger
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-02-01 Released: 2019-06-05
Deposition Author(s): Marshall, S.A., Payne, K.A.P., Leys, D.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.182 (Depositor), 0.183 (DCC)
R-Value Work:
0.161 (Depositor), 0.162 (DCC)
R-Value Observed:
0.162 (Depositor)

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

PubMed: 31142738 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-019-10220-1
Primary Citation 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 _N1 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.

Macromolecule Content

Total Structure Weight: 155 kDa
Atom Count: 9,788
Modeled Residue Count: 1,123
Deposited Residue Count: 1,362
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin prenyltransferase PAD1, mitochondrial	A [auth C] B [auth A] C [auth B] D E A [auth C], B [auth A], C [auth B], D, E, F	227	Aspergillus niger	Mutation(s): 0 Gene Names: PAD1, An03g06570 EC: 2.5.1.129
UniProt
Find proteins for A3F715 (Aspergillus niger) Explore A3F715 Go to UniProtKB: A3F715
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3F715
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain M [auth A] SDF format, chain I [auth C] SDF format, chain H [auth C] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth A] MOL2 format, chain I [auth C] MOL2 format, chain H [auth C] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth A] mmCIF format, chain I [auth C] mmCIF format, chain H [auth C]	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		Interactions Focus chain H [auth C] Focus chain I [auth C] Focus chain M [auth A] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth F] Interactions & Density Focus chain H [auth C] Focus chain I [auth C] Focus chain M [auth A] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth F]
DMA Query on DMA Download:Ideal Coordinates CCD File SDF format, chain U [auth F] SDF format, chain P [auth D] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain J [auth C] SDF format, chain G [auth C] MOL2 format, chain U [auth F] MOL2 format, chain P [auth D] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain J [auth C] MOL2 format, chain G [auth C] mmCIF format, chain U [auth F] mmCIF format, chain P [auth D] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain J [auth C] mmCIF format, chain G [auth C]	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		Interactions Focus chain G [auth C] Focus chain J [auth C] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth D] Focus chain U [auth F] Interactions & Density Focus chain G [auth C] Focus chain J [auth C] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth D] Focus chain U [auth F]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain L [auth A] MOL2 format, chain R [auth D] MOL2 format, chain L [auth A] mmCIF format, chain R [auth D] mmCIF format, chain L [auth A]	L [auth A], R [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain R [auth D] Interactions & Density Focus chain L [auth A] Focus chain R [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.182 (Depositor), 0.183 (DCC)
R-Value Work: 0.161 (Depositor), 0.162 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102	α = 90
b = 102	β = 90
c = 276.69	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-05

Deposition Author(s):

Marshall, S.A.

Payne, K.A.P.

Leys, D.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/K017802/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/P000622/1