7ABW | pdb_00007abw

Crystal structure of siderophore reductase FoxB

PDB DOI: https://doi.org/10.2210/pdb7ABW/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2020-09-09 Released: 2021-09-01
Deposition Author(s): Josts, I., Tidow, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free:
0.299 (Depositor), 0.306 (DCC)
R-Value Work:
0.265 (Depositor), 0.263 (DCC)
R-Value Observed:
0.266 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural insights into a novel family of integral membrane siderophore reductases.

Josts, I., Veith, K., Normant, V., Schalk, I.J., Tidow, H.

(2021) Proc Natl Acad Sci U S A 118

PubMed: 34417315 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2101952118
Primary Citation Related Structures:
7ABW

PubMed Abstract:
Gram-negative bacteria take up the essential ion Fe ³⁺ as ferric-siderophore complexes through their outer membrane using TonB-dependent transporters. However, the subsequent route through the inner membrane differs across many bacterial species and siderophore chemistries and is not understood in detail. Here, we report the crystal structure of the inner membrane protein FoxB (from Pseudomonas aeruginosa ) that is involved in Fe-siderophore uptake. The structure revealed a fold with two tightly bound heme molecules. In combination with in vitro reduction assays and in vivo iron uptake studies, these results establish FoxB as an inner membrane reductase involved in the release of iron from ferrioxamine during Fe-siderophore uptake.

Organizational Affiliation

The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR), 22761 Hamburg, Germany; tidow@chemie.uni-hamburg.de josts@chemie.uni-hamburg.de.

Macromolecule Content

Total Structure Weight: 91.7 kDa
Atom Count: 6,047
Modeled Residue Count: 725
Deposited Residue Count: 764
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PepSY domain-containing protein	A, B	382	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: PA2465 Membrane Entity: Yes
UniProt
Find proteins for Q9I117 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I117 Go to UniProtKB: Q9I117
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I117
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A], D [auth A], J [auth B], K [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B]
DMU Query on DMU Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	F [auth A], G [auth A], L [auth B], M [auth B], N [auth B]	DECYL-BETA-D-MALTOPYRANOSIDE C₂₂ H₄₂ O₁₁ WOQQAWHSKSSAGF-WXFJLFHKSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
PE5 Query on PE5 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C₁₈ H₃₈ O₉ CUDPPTPIUWYGFI-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B]	H [auth A], I [auth A], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free: 0.299 (Depositor), 0.306 (DCC)
R-Value Work: 0.265 (Depositor), 0.263 (DCC)
R-Value Observed: 0.266 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 237.065	α = 90
b = 114.321	β = 90
c = 64.382	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXCD	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-09-01

Deposition Author(s):

Josts, I.

Tidow, H.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History (Full details and data files)

Version 1.0: 2021-09-01
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection
Version 1.2: 2026-01-21
Changes: Database references, Source and taxonomy, Structure summary