7XLZ | pdb_00007xlz

Structure of siderophore-interacting protein from Vibrio anguillarum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 
    0.162 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.138 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.139 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural analysis of the siderophore-interacting protein from Vibrio anguillarum and its implications in classification of Vibrio homologs.

Liu, C.Han, Y.Ma, Q.

(2024) Biochem Biophys Res Commun 739: 150979-150979

  • DOI: https://doi.org/10.1016/j.bbrc.2024.150979
  • Primary Citation of Related Structures:  
    7XLZ

  • PubMed Abstract: 

    Bacteria secrete siderophores to sequester the scarce iron in the environments, then the iron is transported into the cell in a siderophore-complexed form, which can be released by siderophore-interacting protein (SIP). Vibrio species comprise an array of serious pathogens, whose iron releasing process by SIP remains poorly understood. Herein, we report the high-resolution (1.2 Å) structure of Vibrio anguillarum SIP (VaSIP) in complex with FAD, representing the first structure of Vibrio SIP. VaSIP consists of a FAD-bound β-barrel domain and a Rossmann-fold domain connected by a linker, like other subgroup I SIPs. FAD is bound to the inter-domain cavity by aromatic stacking and hydrogen bonding interactions. Structural comparison indicated a modified NAD(P)H-binding motif (DxTA-EVL-GE) for subgroup I SIPs. The putative siderophore-binding pocket of VaSIP contains three lysines to form the basic triad to bind siderophore. Phylogenetic analysis shows Vibrio SIPs are mainly divided into two clades, represented by VaSIP and Vibrio cholerae ViuB, respectively. Interestingly, the two clades adopt distinct siderophore-binding basic triads, suggesting functional divergence among Vibrio SIPs. Our results shed light on the structural and phylogenetic characteristics of Vibrio SIPs, providing molecular basis for understanding Vibrio iron metabolism and designing anti-Vibrio drugs.


  • Organizational Affiliation

    CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Siderophore-interacting protein
A, B
266Vibrio anguillarum 775Mutation(s): 0 
Gene Names: VAA_01637
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free:  0.162 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.138 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.139 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.622α = 90
b = 58.466β = 114.18
c = 70.65γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-12-11
    Changes: Database references, Structure summary