5OE3 | pdb_00005oe3

Crystal structure of the N-terminal domain of PqsA in complex with anthraniloyl-AMP (crystal form 1)

PDB DOI: https://doi.org/10.2210/pdb5OE3/pdb

Classification: LIGASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-07-07 Released: 2017-09-06
Deposition Author(s): Witzgall, F., Ewert, W., Blankenfeldt, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structures of the N-Terminal Domain of PqsA in Complex with Anthraniloyl- and 6-Fluoroanthraniloyl-AMP: Substrate Activation in Pseudomonas Quinolone Signal (PQS) Biosynthesis.

Witzgall, F., Ewert, W., Blankenfeldt, W.

(2017) Chembiochem 18: 2045-2055

PubMed: 28834007 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201700374
Primary Citation Related Structures:
5OE3, 5OE4, 5OE5, 5OE6

PubMed Abstract:
Pseudomonas aeruginosa, a prevalent pathogen in nosocomial infections and a major burden in cystic fibrosis, uses three interconnected quorum-sensing systems to coordinate virulence processes. At variance with other Gram-negative bacteria, one of these systems relies on 2-alkyl-4(1H)-quinolones (Pseudomonas quinolone signal, PQS) and might hence be an attractive target for new anti-infective agents. Here we report crystal structures of the N-terminal domain of anthranilate-CoA ligase PqsA, the first enzyme of PQS biosynthesis, in complex with anthraniloyl-AMP and with 6-fluoroanthraniloyl-AMP (6FABA-AMP) at 1.4 and 1.7 Å resolution. We find that PqsA belongs to an unrecognized subfamily of anthranilate-CoA ligases that recognize the amino group of anthranilate through a water-mediated hydrogen bond. The complex with 6FABA-AMP explains why 6FABA, an inhibitor of PQS biosynthesis, is a good substrate of PqsA. Together, our data might pave a way to new pathoblockers in P. aeruginosa infections.

Organizational Affiliation

Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.

Macromolecule Content

Total Structure Weight: 181.36 kDa
Atom Count: 15,391
Modeled Residue Count: 1,574
Deposited Residue Count: 1,628
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anthranilate--CoA ligase	A, B, C, D	407	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: pqsA, PA0996 EC: 6.2.1.32
UniProt
Find proteins for Q9I4X3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I4X3 Go to UniProtKB: Q9I4X3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I4X3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3UK Query on 3UK Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain Y [auth D] SDF format, chain T [auth C] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain T [auth C] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain T [auth C]	E [auth A], M [auth B], T [auth C], Y [auth D]	5'-O-[(S)-[(2-aminobenzoyl)oxy](hydroxy)phosphoryl]adenosine C₁₇ H₁₉ N₆ O₈ P XZXXWUQOHYJTTC-XNIJJKJLSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] MOL2 format, chain EA [auth D] mmCIF format, chain EA [auth D]	EA [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Interactions & Density Focus chain EA [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain S [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth D] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain S [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain S [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain G [auth A]	F [auth A] G [auth A] H [auth A] S [auth C] U [auth C] F [auth A], G [auth A], H [auth A], S [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Z [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain DA [auth D] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain DA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] I [auth A] AA [auth D], BA [auth D], CA [auth D], DA [auth D], I [auth A], J [auth A], K [auth A], L [auth A], N [auth B], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.216 (Depositor), 0.216 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.533	α = 90
b = 84.448	β = 92.6
c = 139.011	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-09-06

Deposition Author(s):

Witzgall, F.

Ewert, W.

Blankenfeldt, W.

Revision History (Full details and data files)

Version 1.0: 2017-09-06
Type: Initial release
Version 1.1: 2017-10-25
Changes: Database references
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Refinement description

5OE3 | pdb_00005oe3

Crystal structure of the N-terminal domain of PqsA in complex with anthraniloyl-AMP (crystal form 1)

Literature

Structures of the N-Terminal Domain of PqsA in Complex with Anthraniloyl- and 6-Fluoroanthraniloyl-AMP: Substrate Activation in Pseudomonas Quinolone Signal (PQS) Biosynthesis.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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