6HAI

AlbAM131A mutant in complex with albicidin , albicidin resistance protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Adaptation of a Bacterial Multidrug Resistance System Revealed by the Structure and Function of AlbA.

Sikandar, A.Cirnski, K.Testolin, G.Volz, C.Bronstrup, M.Kalinina, O.V.Muller, R.Koehnke, J.

(2018) J Am Chem Soc 140: 16641-16649

  • DOI: https://doi.org/10.1021/jacs.8b08895
  • Primary Citation of Related Structures:  
    6H95, 6H96, 6H97, 6HAI

  • PubMed Abstract: 
  • To combat the rise of antimicrobial resistance, the discovery of new antibiotics is paramount. Albicidin and cystobactamid are related natural product antibiotics with potent activity against Gram-positive and, crucially, Gram-negative pathogens. AlbA has been reported to neutralize albicidin by binding it with nanomolar affinity ...

    To combat the rise of antimicrobial resistance, the discovery of new antibiotics is paramount. Albicidin and cystobactamid are related natural product antibiotics with potent activity against Gram-positive and, crucially, Gram-negative pathogens. AlbA has been reported to neutralize albicidin by binding it with nanomolar affinity. To understand this potential resistance mechanism, we determined structures of AlbA and its complex with albicidin. The structures revealed AlbA to be comprised of two domains, each unexpectedly resembling the multiantibiotic neutralizing protein TipA. Binding of the long albicidin molecule was shared pseudosymmetrically between the two domains. The structure also revealed an unexpected chemical modification of albicidin, which we demonstrate to be promoted by AlbA, and to reduce albicidin potency; we propose a mechanism for this reaction. Overall, our findings suggest that AlbA arose through internal duplication in an ancient TipA-like gene, leading to a new binding scaffold adapted to the sequestration of long-chain antibiotics.


    Organizational Affiliation

    Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland , Helmholtz Centre for Infection Research, Saarland University , Campus Geb. E8.1 , Saarbrücken 66123 , Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Albicidin resistance protein
A, B
226Klebsiella oxytocaMutation(s): 0 
Gene Names: albA
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FWW
Query on FWW

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
4-[[4-[[4-[(3~{S})-3-[[4-[[(~{E})-3-(4-hydroxyphenyl)-2-methyl-prop-2-enoyl]amino]phenyl]carbonylamino]-2,5-bis(oxidanylidene)pyrrolidin-1-yl]phenyl]carbonylamino]-3-methoxy-2-oxidanyl-phenyl]carbonylamino]-3-methoxy-2-oxidanyl-benzoic acid
C44 H37 N5 O13
XOWPHBSEUBUKBU-QCKJEFJWSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.26α = 90
b = 123.497β = 90
c = 161.171γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
GermanyKO4116_3_1

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references