7ABN

Structure of the reversible pyrrole-2-carboxylic acid decarboxylase PA0254/HudA

PDB DOI: https://doi.org/10.2210/pdb7ABN/pdb

Classification: LIGASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-09-08 Released: 2021-04-07
Deposition Author(s): Leys, D.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.235
R-Value Work: 0.201
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure and Mechanism of Pseudomonas aeruginosa PA0254/HudA, a prFMN-Dependent Pyrrole-2-carboxylic Acid Decarboxylase Linked to Virulence.

Payne, K.A.P., Marshall, S.A., Fisher, K., Rigby, S.E.J., Cliff, M.J., Spiess, R., Cannas, D.M., Larrosa, I., Hay, S., Leys, D.

(2021) ACS Catal 11: 2865-2878

PubMed: 33763291 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acscatal.0c05042
Primary Citation of Related Structures:
7ABN, 7ABO

PubMed Abstract:
The UbiD family of reversible (de)carboxylases depends on the recently discovered prenylated-FMN (prFMN) cofactor for activity. The model enzyme ferulic acid decarboxylase (Fdc1) decarboxylates unsaturated aliphatic acids via a reversible 1,3-cycloaddition process. Protein engineering has extended the Fdc1 substrate range to include (hetero)aromatic acids, although catalytic rates remain poor. This raises the question how efficient decarboxylation of (hetero)aromatic acids is achieved by other UbiD family members. Here, we show that the Pseudomonas aeruginosa virulence attenuation factor PA0254 / HudA is a pyrrole-2-carboxylic acid decarboxylase. The crystal structure of the enzyme in the presence of the reversible inhibitor imidazole reveals a covalent prFMN - imidazole adduct is formed. Substrate screening reveals HudA and selected active site variants can accept a modest range of heteroaromatic compounds, including thiophene-2-carboxylic acid. Together with computational studies, our data suggests prFMN covalent catalysis occurs via electrophilic aromatic substitution and links HudA activity with the inhibitory effects of pyrrole-2-carboxylic acid on P. aeruginosa quorum sensing.

Organizational Affiliation

Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.

Macromolecule Content

Total Structure Weight: 221.01 kDa
Atom Count: 16,967
Modelled Residue Count: 1,980
Deposited Residue Count: 1,984
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UbiD-like decarboxylase	A [auth D], B [auth A], C [auth H], D [auth M]	496	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: ECC04_013425 EC: 4.1.1
UniProt
Find proteins for Q9I6N5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I6N5 Go to UniProtKB: Q9I6N5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I6N5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4LU (Subject of Investigation/LOI) Query on 4LU Download Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain K [auth A] SDF format, chain O [auth H] SDF format, chain T [auth M] MOL2 format, chain G [auth D] MOL2 format, chain K [auth A] MOL2 format, chain O [auth H] MOL2 format, chain T [auth M]	G [auth D], K [auth A], O [auth H], T [auth M]	1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol C₂₂ H₃₀ N₄ O₉ P KOUJZPGFPGLHCZ-IYOUNJFTSA-O		Interactions Focus chain G [auth D] Focus chain K [auth A] Focus chain O [auth H] Focus chain T [auth M] Interactions & Density Focus chain G [auth D] Focus chain K [auth A] Focus chain O [auth H] Focus chain T [auth M]
IMD (Subject of Investigation/LOI) Query on IMD Download Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain L [auth A] SDF format, chain P [auth H] SDF format, chain Q [auth M] MOL2 format, chain H [auth D] MOL2 format, chain L [auth A] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth M]	H [auth D], L [auth A], P [auth H], Q [auth M]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain H [auth D] Focus chain L [auth A] Focus chain P [auth H] Focus chain Q [auth M] Interactions & Density Focus chain H [auth D] Focus chain L [auth A] Focus chain P [auth H] Focus chain Q [auth M]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain I [auth A] SDF format, chain M [auth H] SDF format, chain R [auth M] MOL2 format, chain E [auth D] MOL2 format, chain I [auth A] MOL2 format, chain M [auth H] MOL2 format, chain R [auth M]	E [auth D], I [auth A], M [auth H], R [auth M]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth D] Focus chain I [auth A] Focus chain M [auth H] Focus chain R [auth M] Interactions & Density Focus chain E [auth D] Focus chain I [auth A] Focus chain M [auth H] Focus chain R [auth M]
K Query on K Download Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain J [auth A] SDF format, chain N [auth H] SDF format, chain S [auth M] MOL2 format, chain F [auth D] MOL2 format, chain J [auth A] MOL2 format, chain N [auth H] MOL2 format, chain S [auth M]	F [auth D], J [auth A], N [auth H], S [auth M]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Focus chain J [auth A] Focus chain N [auth H] Focus chain S [auth M] Interactions & Density Focus chain F [auth D] Focus chain J [auth A] Focus chain N [auth H] Focus chain S [auth M]