1QKC

ESCHERICHIA COLI FERRIC HYDROXAMATE UPTAKE RECEPTOR (FHUA) IN COMPLEX DELTA TWO-ALBOMYCIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of the antibiotic albomycin in complex with the outer membrane transporter FhuA.

Ferguson, A.D.Braun, V.Fiedler, H.P.Coulton, J.W.Diederichs, K.Welte, W.

(2000) Protein Sci 9: 956-963

  • DOI: 10.1110/ps.9.5.956
  • Primary Citation of Related Structures:  
    1QJQ, 1QKC

  • PubMed Abstract: 
  • One alternative method for drug delivery involves the use of siderophore-antibiotic conjugates. These compounds represent a specific means by which potent antimicrobial agents, covalently linked to iron-chelating siderophores, can be actively transported across the outer membrane of gram-negative bacteria ...

    One alternative method for drug delivery involves the use of siderophore-antibiotic conjugates. These compounds represent a specific means by which potent antimicrobial agents, covalently linked to iron-chelating siderophores, can be actively transported across the outer membrane of gram-negative bacteria. These "Trojan Horse" antibiotics may prove useful as an efficient means to combat multi-drug-resistant bacterial infections. Here we present the crystallographic structures of the natural siderophore-antibiotic conjugate albomycin and the siderophore phenylferricrocin, in complex with the active outer membrane transporter FhuA from Escherichia coli. To our knowledge, this represents the first structure of an antibiotic bound to its cognate transporter. Albomycins are broad-host range antibiotics that consist of a hydroxamate-type iron-chelating siderophore, and an antibiotically active, thioribosyl pyrimidine moiety. As observed with other hydroxamate-type siderophores, the three-dimensional structure of albomycin reveals an identical coordination geometry surrounding the ferric iron atom. Unexpectedly, this antibiotic assumes two conformational isomers in the binding site of FhuA, an extended and a compact form. The structural information derived from this study provides novel insights into the diverse array of antibiotic moieties that can be linked to the distal portion of iron-chelating siderophores and offers a structural platform for the rational design of hydroxamate-type siderophore-antibiotic conjugates.


    Related Citations: 
    • An Internal Affinity-Tag for Purification and Crystallization of the Siderophore Receptor Fhua, Integral Outer Membrane Protein from Escherichia Coli K-12
      Ferguson, A.D., Breed, J., Diederichs, K., Welte, W., Coulton, J.W.
      (1998) Protein Sci 7: 1636
    • Siderophore-Mediated Iron Transport: Crystal Structure of Fhua with Bound Lipopolysaccharide
      Ferguson, A.D., Hofmann, E., Coulton, J.W., Diederichs, K., Welte, W.
      (1998) Science 282: 2215

    Organizational Affiliation

    Fachbereich Biologie, Universität Konstanz, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FERRIC HYDROXAMATE RECEPTORA725Escherichia coli K-12Mutation(s): 0 
Gene Names: fhuAtonAb0150JW0146
Membrane Entity: Yes 
UniProt
Find proteins for P06971 (Escherichia coli (strain K12))
Explore P06971 
Go to UniProtKB:  P06971
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06971
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-[L-glycero-alpha-D-manno-heptopyranose-(1-7)]L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2,3-dideoxy-alpha-D-glucoyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranoseB 11N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G08252UR
GlyCosmos:  G08252UR
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ALB
Query on ALB

Download Ideal Coordinates CCD File 
N [auth A]DELTA-2-ALBOMYCIN A1
C37 H57 Fe N12 O18 S
RQZRKFJHRUDTLB-BMLDZKGGDD
 Ligand Interaction
FTT
Query on FTT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
3-HYDROXY-TETRADECANOIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
 Ligand Interaction
DPO
Query on DPO

Download Ideal Coordinates CCD File 
I [auth A],
K [auth A]
DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
J [auth A],
L [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
M [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.8α = 90
b = 171.8β = 90
c = 86.35γ = 120
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2018-03-07
    Changes: Source and taxonomy
  • Version 1.5: 2019-10-09
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.6: 2020-07-01
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary