2H1O

Structure of FitAB bound to IR36 DNA fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.269 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs.

Mattison, K.Wilbur, J.S.So, M.Brennan, R.G.

(2006) J Biol Chem 281: 37942-37951

  • DOI: 10.1074/jbc.M605198200
  • Primary Citation of Related Structures:  
    2BSQ, 2H1O, 2H1C

  • PubMed Abstract: 
  • Neisseria gonorrhoeae is a sexually transmitted pathogen that initiates infections in humans by adhering to the mucosal epithelium of the urogenital tract. The bacterium then enters the apical region of the cell and traffics across the cell to exit into the subepithelial matrix ...

    Neisseria gonorrhoeae is a sexually transmitted pathogen that initiates infections in humans by adhering to the mucosal epithelium of the urogenital tract. The bacterium then enters the apical region of the cell and traffics across the cell to exit into the subepithelial matrix. Mutations in the fast intracellular trafficking (fitAB) locus cause the bacteria to transit a polarized epithelial monolayer more quickly than the wild-type parent and to replicate within cells at an accelerated rate. Here, we describe the crystal structure of the toxin-antitoxin heterodimer, FitAB, bound to a high affinity 36-bp DNA fragment from the fitAB promoter. FitA, the antitoxin, binds DNA through its ribbon-helix-helix motif and is tethered to FitB, the toxin, to form a heterodimer by the insertion of a four turn alpha-helix into an extensive FitB hydrophobic pocket. FitB is composed of a PIN (PilT N terminus) domain, with a central, twisted, 5-stranded parallel beta-sheet that is open on one side and flanked by five alpha-helices. FitB in the context of the FitAB complex does not display nuclease activity against tested PIN substrates. The FitAB complex points to the mechanism by which antitoxins with RHH motifs can block the activity of toxins with PIN domains. Interactions between two FitB molecules result in the formation of a tetramer of FitAB heterodimers, which binds to the 36-bp DNA fragment and provides an explanation for how FitB enhances the DNA binding affinity of FitA.


    Organizational Affiliation

    Department of Biochemistry, Oregon Health and Science University, Portland, Oregon 97239, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Trafficking protein BC [auth A], D [auth B], E [auth C], F [auth D]143Neisseria gonorrhoeaeMutation(s): 3 
Gene Names: fitB
EC: 3.1
UniProt
Find proteins for Q5F882 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090))
Explore Q5F882 
Go to UniProtKB:  Q5F882
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Trafficking protein AG [auth E], H [auth F], I [auth G], J [auth H]68Neisseria gonorrhoeaeMutation(s): 0 
Gene Names: fitA
UniProt
Find proteins for Q5F881 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090))
Explore Q5F881 
Go to UniProtKB:  Q5F881
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
IR36-strand 1A [auth U]36N/A
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
IR36-strand 2B [auth V]36N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.269 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.04α = 90
b = 82.403β = 94.19
c = 135.503γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-02-06
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance