8VUK | pdb_00008vuk

The crystal structure of Brucella abortus FtrB at 1.3 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb8VUK/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Brucella abortus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-01-29 Released: 2025-01-22 
• Deposition Author(s): Roy, S., Garcia, B.L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: in silico

Literature

In Vitro Structural and Functional Studies of a Novel Cupredoxin, FtrB, from Brucella abortus 2308.

Kerkan, A., Hart, K., Martin, D.W., Pajski, J., Aidoo, B., Garcia, B.L., Roy, S., Dasgupta, S., Hematian, S., Santisteban-Veiga, A., Schaaf, N.J., Banerjee, S.

(2025) ACS Omega 10: 12653-12670

• PubMed: 40191301 
• DOI: https://doi.org/10.1021/acsomega.5c00690
• Primary Citation Related Structures: 
  8VUK


• PubMed Abstract: 
  

  FtrABCD is a four-component iron transporter found in several Gram-negative bacteria. Previous data confirm that FtrABCD can only utilize Fe ²⁺ and the inner membrane permease, FtrC, from this system, like its eukaryotic homologue, Ftr1p, is predicted to utilize the free energy released during Fe ²⁺ oxidation for the transport. Periplasmic FtrB from this system is coancestral with known copper oxidases, and the conserved D118 and H121 are predicted to bind to Cu ²⁺ , forming an active enzyme. In this work, we report structural data for recombinant wild-type and D118A and H121A mutants from Brucella abortus 2308 which confirm a β-sheet-rich structure which is distinct from known cupredoxins. Calorimetric studies on the wild-type protein show μM affinities for Cu ²⁺ and an Fe ²⁺ mimic (Mn ²⁺ ), which facilitate the formation of the active enzyme and the enzyme-substrate complex, respectively. In contrast, the D118A mutant failed to bind Cu ²⁺ . Finally, the electrochemical data reported here revealed biologically accessible reduction potentials for the Cu ²⁺ ion in the active enzyme which also showed a pseudozero-order rate of Fe ²⁺ oxidation at pH 6.5 and could oxidize Fe ²⁺ 3.5-times faster than its rate of autoxidation. Taken together, this report provides experimental data that support structural and functional predictions of FtrB under in vitro conditions.

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Organizational Affiliation: 
• Department of Chemistry, East Carolina University, Science and Technology Building, Room 409, Greenville, North Carolina 27858, United States.
Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina 27852, United States.
Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States.
Department of Chemistry, Amity University Kolkata, Kolkata, WB 700134, India.
Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States.
AFFINImeter Scientific & Development Team, Software 4 Science Developments, Avenida do Mestre Mateo, 2, 15706 Santiago de Compostela, A Coruña, Spain.
University of Santiago de Compostela, Santiago de Compostela 15782, Spain.
University of Santiago de Compostela, Rúa de José María Suárez Núñez, s/n, 15782 Santiago de Compostela, A Coruña, Spain.
Colloids and Polymers Physics Group, Institute of Materials (iMATUS), Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, A Coruña, Spain.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 10.31 kDa 
• Atom Count: 842 
• Modeled Residue Count: 89 
• Deposited Residue Count: 90 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EfeO-type cupredoxin-like domain-containing protein	A	90	Brucella abortus	Mutation(s): 0  Gene Names: BAbS19_II07770
UniProt
Find proteins for Q2YK41 (Brucella abortus (strain 2308)) Explore Q2YK41  Go to UniProtKB:  Q2YK41

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.811	α = 83.41
b = 27.033	β = 69.64
c = 30.821	γ = 71.81

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Roy, S., Garcia, B.L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release
  
• Version 1.1: 2025-08-06
  Changes: Database references