9HRP | pdb_00009hrp

Structure of YIUA from Yersinia ruckeri with iron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 
    0.287 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

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


Literature

Yersinia ruckeri YRB periplasmic binding protein YiuA selectively recognizes a Fe(III)-mono-catecholate siderophore.

Thomsen, E.Thompson, S.Stow, P.R.Cukor, M.Grogan, G.Duhme-Klair, A.K.Butler, A.

(2025) Chem Commun (Camb) 61: 17653-17656

  • DOI: https://doi.org/10.1039/d5cc05103g
  • Primary Citation of Related Structures:  
    9HRP, 9IF3

  • PubMed Abstract: 

    The marine pathogen Yersinia ruckeri synthesizes the tri-catecholate siderophore ruckerbactin, Rb, (DHB- L Arg- L Ser) 3 , to acquire iron during infection. Its biosynthetic gene cluster encodes a single periplasmic binding protein, RupB, which surprisingly does not bind Fe(III)-Rb nor the Fe(III) complexes of its hydrolysis products, the di- and mono-catecholate siderophores Rb DC and Rb MC , with biologically relevant affinities. Instead, the periplasmic binding protein YiuA, encoded in a different region of the chromosome, binds the 1 : 2 Fe(III) complex of the mono-catecholate Rb MC , Fe(III)-(Rb MC ) 2 . YiuA is the first periplasmic binding protein (PBP) to selectively recognize a mono-catecholate siderophore, the structural basis of which was illuminated through X-ray crystallography of YiuA bound to Fe(III)-(Rb MC ) 2 .


  • Organizational Affiliation
    • University of California, Department of Chemistry & Biochemistry, Santa Barbara, CA 93106-9510, USA. butler@chem.ucsb.edu.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic substrate-binding transport protein
A, B, C, D
349Yersinia ruckeriMutation(s): 0 
Gene Names: CSF007_11785
UniProt
Find proteins for A0A085U4N5 (Yersinia ruckeri)
Explore A0A085U4N5 
Go to UniProtKB:  A0A085U4N5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A085U4N5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free:  0.287 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.494α = 90
b = 76.228β = 95.06
c = 99.926γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Database references
  • Version 1.2: 2025-11-19
    Changes: Database references