8VWN

Crystal structure of Vibrio cholerae NFeoB in the GDP-bound form

PDB DOI: https://doi.org/10.2210/pdb8VWN/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Vibrio cholerae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-01 Released: 2024-10-30
Deposition Author(s): Lee, M., Smith, A.T.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.25 Å
R-Value Free: 0.269
R-Value Work: 0.221
R-Value Observed: 0.224

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural determinants of Vibrio cholerae FeoB nucleotide promiscuity.

Lee, M., Magante, K., Gomez-Garzon, C., Payne, S.M., Smith, A.T.

(2024) J Biol Chem 300: 107663-107663

PubMed: 39128725 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2024.107663
Primary Citation of Related Structures:
8VWL, 8VWN, 9BA6, 9BA7

PubMed Abstract:
Ferrous iron (Fe ²⁺) is required for the growth and virulence of many pathogenic bacteria, including Vibrio cholerae (Vc), the causative agent of the disease cholera. For this bacterium, Feo is the primary system that transports Fe ²⁺ into the cytosol. FeoB, the main component of this system, is regulated by a soluble cytosolic domain termed NFeoB. Recent reanalysis has shown that NFeoBs can be classified as either GTP-specific or NTP-promiscuous, but the structural and mechanistic bases for these differences were not known. To explore this intriguing property of FeoB, we solved the X-ray crystal structures of VcNFeoB in both the apo and the GDP-bound forms. Surprisingly, this promiscuous NTPase displayed a canonical NFeoB G-protein fold like GTP-specific NFeoBs. Using structural bioinformatics, we hypothesized that residues surrounding the nucleobase could be important for both nucleotide affinity and specificity. We then solved the X-ray crystal structures of N150T VcNFeoB in the apo and GDP-bound forms to reveal H-bonding differences surrounding the guanine nucleobase. Interestingly, isothermal titration calorimetry revealed similar binding thermodynamics of the WT and N150T proteins to guanine nucleotides, while the behavior in the presence of adenine nucleotides was dramatically different. AlphaFold models of VcNFeoB in the presence of ADP and ATP showed important conformational changes that contribute to nucleotide specificity among FeoBs. Combined, these results provide a structural framework for understanding FeoB nucleotide promiscuity, which could be an adaptive measure utilized by pathogens to ensure adequate levels of intracellular iron across multiple metabolic landscapes.

Organizational Affiliation

Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA.

Macromolecule Content

Total Structure Weight: 130.45 kDa
Atom Count: 7,888
Modelled Residue Count: 979
Deposited Residue Count: 1,140
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferrous iron transport protein B	A, B, C, D	285	Vibrio cholerae	Mutation(s): 0 Gene Names: feoB_1, ERS013165_00117
UniProt
Find proteins for A0A655NVH2 (Vibrio cholerae) Explore A0A655NVH2 Go to UniProtKB: A0A655NVH2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A655NVH2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth D] SDF format, chain G [auth B] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth D] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth D] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C]	E [auth A], G [auth B], I [auth C], J [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain K [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth D]	F [auth A], H [auth B], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.25 Å
R-Value Free: 0.269
R-Value Work: 0.221
R-Value Observed: 0.224
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 194.27	α = 90
b = 155.309	β = 95.88
c = 50.916	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

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-30

Deposition Author(s):

Lee, M.

Smith, A.T.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM133497
National Science Foundation (NSF, United States)	United States	CHE1844624