9IF3 | pdb_00009if3

Structure of YIUA from Yersinia ruckeri with Iron and DHB-L-Arg-L-Ser

PDB DOI: https://doi.org/10.2210/pdb9IF3/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Yersinia ruckeri
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-02-17 Released: 2025-11-05
Deposition Author(s): Thompson, S., Thomsen, E., Duhme-Klair, A., Butler, A., Grogan, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.277 (Depositor), 0.284 (DCC)
R-Value Work:
0.247 (Depositor), 0.252 (DCC)
R-Value Observed:
0.248 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 41098114 Search on PubMed
DOI: https://doi.org/10.1039/d5cc05103g
Primary Citation Related Structures:
9HRP, 9IF3

PubMed Abstract:
The marine pathogen Yersinia ruckeri synthesizes the tri-catecholate siderophore ruckerbactin, Rb, (DHB- ^LArg- ^LSer) 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.

Macromolecule Content

Total Structure Weight: 314.69 kDa
Atom Count: 21,896
Modeled Residue Count: 2,771
Deposited Residue Count: 2,792
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic substrate-binding transport protein	A, B, C, D, E A, B, C, D, E, F, G, H	349	Yersinia ruckeri	Mutation(s): 0 Gene Names: CSF007_11785
UniProt
Find proteins for A0A085U4N5 (Yersinia ruckeri) Explore A0A085U4N5 Go to UniProtKB: A0A085U4N5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A085U4N5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1I15 (Subject of Investigation/LOI) Query on A1I15 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth F] SDF format, chain K [auth A] SDF format, chain KA [auth F] SDF format, chain O [auth B] SDF format, chain OA [auth G] SDF format, chain P [auth B] SDF format, chain PA [auth G] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain VA [auth H] SDF format, chain WA [auth H] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth G] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain VA [auth H] MOL2 format, chain WA [auth H] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth G] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain VA [auth H] mmCIF format, chain WA [auth H] mmCIF format, chain Z [auth D]	AA [auth D] EA [auth E] FA [auth E] J [auth A] JA [auth F] AA [auth D], EA [auth E], FA [auth E], J [auth A], JA [auth F], K [auth A], KA [auth F], O [auth B], OA [auth G], P [auth B], PA [auth G], S [auth C], T [auth C], VA [auth H], WA [auth H], Z [auth D]	(2~{S})-2-[[(2~{S})-2-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-5-carbamimidamido-pentanoyl]amino]-3-oxidanyl-propanoic acid C₁₆ H₂₃ N₅ O₇ LXNCWECCTQQXPQ-UWVGGRQHSA-N		Interactions Focus chain AA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain O [auth B] Focus chain OA [auth G] Focus chain P [auth B] Focus chain PA [auth G] Focus chain S [auth C] Focus chain T [auth C] Focus chain VA [auth H] Focus chain WA [auth H] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain O [auth B] Focus chain OA [auth G] Focus chain P [auth B] Focus chain PA [auth G] Focus chain S [auth C] Focus chain T [auth C] Focus chain VA [auth H] Focus chain WA [auth H] Focus chain Z [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth F] SDF format, chain M [auth A] SDF format, chain MA [auth F] SDF format, chain Q [auth B] SDF format, chain QA [auth G] SDF format, chain RA [auth G] SDF format, chain SA [auth G] SDF format, chain TA [auth G] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain XA [auth H] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain RA [auth G] MOL2 format, chain SA [auth G] MOL2 format, chain TA [auth G] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth H] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth G] mmCIF format, chain RA [auth G] mmCIF format, chain SA [auth G] mmCIF format, chain TA [auth G] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth H]	BA [auth D] CA [auth D] GA [auth E] HA [auth E] L [auth A] BA [auth D], CA [auth D], GA [auth E], HA [auth E], L [auth A], LA [auth F], M [auth A], MA [auth F], Q [auth B], QA [auth G], RA [auth G], SA [auth G], TA [auth G], U [auth C], V [auth C], W [auth C], X [auth C], XA [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain XA [auth H] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain XA [auth H]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain NA [auth G] SDF format, chain R [auth C] SDF format, chain UA [auth H] SDF format, chain Y [auth D] SDF format, chain IA [auth F] MOL2 format, chain DA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth G] MOL2 format, chain R [auth C] MOL2 format, chain UA [auth H] MOL2 format, chain Y [auth D] MOL2 format, chain IA [auth F] mmCIF format, chain DA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth G] mmCIF format, chain R [auth C] mmCIF format, chain UA [auth H] mmCIF format, chain Y [auth D] mmCIF format, chain IA [auth F]	DA [auth E] I [auth A] IA [auth F] N [auth B] NA [auth G] DA [auth E], I [auth A], IA [auth F], N [auth B], NA [auth G], R [auth C], UA [auth H], Y [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain N [auth B] Focus chain NA [auth G] Focus chain R [auth C] Focus chain UA [auth H] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain N [auth B] Focus chain NA [auth G] Focus chain R [auth C] Focus chain UA [auth H] Focus chain Y [auth D]