Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 34.25 kDa 
• Atom Count: 2713 
• Residue Count: 301 
• Unique protein chains: 1

3R5S

Crystal structure of apo-ViuP

• DOI: 10.2210/pdb3R5S/pdb

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


• Deposited: 2011-03-19 Released: 2012-02-08 
• Deposition Author(s): Li, N., Zhang, C., Li, B., Liu, X., Huang, Y., Xu, S., Gu, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.213 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 

Literature

Unique iron coordination in iron-chelating molecule vibriobactin helps Vibrio cholerae evade mammalian siderocalin-mediated immune response.

Li, N., Zhang, C., Li, B., Liu, X., Huang, Y., Xu, S., Gu, L.

(2012) J Biol Chem 287: 8912-8919

• PubMed: 22291019 
• DOI: 10.1074/jbc.M111.316034
• Primary Citation of Related Structures:  
  3R5S, 3R5T


• PubMed Abstract: 
  

Iron is essential for the survival of almost all bacteria. Vibrio cholerae acquires iron through the secretion of a catecholate siderophore called vibriobactin. At present, how vibriobactin chelates ferric ion remains controversial. In addition, the mechanisms underlying the recognition of ferric vibriobactin by the siderophore transport system and its delivery into the cytoplasm specifically have not been clarified. In this study, we report the high-resolution structures of the ferric vibriobactin periplasmic binding protein ViuP and its complex with ferric vibriobactin. The holo-ViuP structure reveals that ferric vibriobactin does not adopt the same iron coordination as that of other catecholate siderophores such as enterobactin. The three catechol moieties donate five, rather than six, oxygen atoms as iron ligands. The sixth iron ligand is provided by a nitrogen atom from the second oxazoline ring. This kind of iron coordination results in the protrusion of the second catechol moiety and renders the electrostatic surface potential of ferric vibriobactin less negatively polarized compared with ferric enterobactin. To accommodate ferric vibriobactin, ViuP has a deeper subpocket to hold the protrusion of the second catechol group. This structural characteristic has not been observed in other catecholate siderophore-binding proteins. Biochemical data show that siderocalin, which is part of the mammalian innate immune system, cannot efficiently sequester ferric vibriobactin in vitro, although it can capture many catecholate siderophores with high efficiency. Our findings suggest that the unique iron coordination found in ferric vibriobactin may be utilized by some pathogenic bacteria to evade the siderocalin-mediated innate immune response of mammals.

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Organizational Affiliation: 

State Key Laboratory of Microbial Technology, Shandong University, Jinan, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferric vibriobactin ABC transporter, periplasmic ferric vibriobactin-binding protein	A	305	Vibrio cholerae	Mutation(s): 0  Gene Names: viuP, VC_0776, C9J66_11805, D6U80_13395, ERS013140_02227, ERS013165_02595, ERS013186_02145, ERS013199_00569, ERS013202_00573, ERS013206_00558
Find proteins for Q9RCF6 (Vibrio cholerae) Explore Q9RCF6  Go to UniProtKB:  Q9RCF6

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.213 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.925	α = 90
b = 61.068	β = 120.56
c = 66.852	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-19 
• Released Date: 2012-02-08 
Deposition Author(s): Li, N., Zhang, C., Li, B., Liu, X., Huang, Y., Xu, S., Gu, L.

Revision History 

• Version 1.0: 2012-02-08
  Type: Initial release
  
• Version 1.1: 2012-05-30
  Changes: Database references