PDBsum entry 1f36

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protein Protein-protein interface(s) links
Transactivation region PDB id
Protein chains
89 a.a. *
Waters ×66
* Residue conservation analysis
PDB id:
Name: Transactivation region
Title: The crystal structure of fis mutant k36e reveals that the transactivation region of the fis protein contains extended mobile beta-hairpin arms
Structure: Fis. Chain: a, b. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: ymel. Cell_line: bl21. Gene: fis. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Dimer (from PDB file)
2.65Å     R-factor:   0.222     R-free:   0.277
Authors: M.K.Safo,H.S.Yuan
Key ref:
M.K.Safo et al. (1997). The transactivation region of the fis protein that controls site-specific DNA inversion contains extended mobile beta-hairpin arms. EMBO J, 16, 6860-6873. PubMed id: 9362499 DOI: 10.1093/emboj/16.22.6860
20-Jun-97     Release date:   24-Dec-97    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0A6R3  (FIS_ECOLI) -  DNA-binding protein Fis
98 a.a.
89 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasmic nucleosome   1 term 
  Biological process     regulation of transcription by chromatin organization   3 terms 
  Biochemical function     protein binding     4 terms  


DOI no: 10.1093/emboj/16.22.6860 EMBO J 16:6860-6873 (1997)
PubMed id: 9362499  
The transactivation region of the fis protein that controls site-specific DNA inversion contains extended mobile beta-hairpin arms.
M.K.Safo, W.Z.Yang, L.Corselli, S.E.Cramton, H.S.Yuan, R.C.Johnson.
The Fis protein regulates site-specific DNA inversion catalyzed by a family of DNA invertases when bound to a cis-acting recombinational enhancer. As is often found for transactivation domains, previous crystal structures have failed to resolve the conformation of the N-terminal inversion activation region within the Fis dimer. A new crystal form of a mutant Fis protein now reveals that the activation region contains two beta-hairpin arms that protrude over 20 A from the protein core. Saturation mutagenesis identified the regulatory and structurally important amino acids. The most critical activating residues are located near the tips of the beta-arms. Disulfide cross-linking between the beta-arms demonstrated that they are highly flexible in solution and that efficient inversion activation can occur when the beta-arms are covalently linked together. The emerging picture for this regulatory motif is that contacts with the recombinase at the tip of the mobile beta-arms activate the DNA invertase in the context of an invertasome complex.
  Selected figure(s)  
Figure 2.
Figure 2 Activation of Hin-catalyzed DNA inversion by Fis mutants with amino acid substitutions in the -hairpin loop region. In vitro inversion reactions were incubated for 1 min followed by digestion of the DNA with restriction enzymes to determine the orientation of the invertible segment. (par) indicates the location of DNA fragments in the parental orientation; (inv) indicates the location of DNA fragments in the inverted orientation after agarose gel electrophoresis. The Fis mutants used in each reaction are listed on the top, with NEM designating after alkylation with N-ethylmaleimide. WT indicates wild-type and (-) indicates no Fis added.
Figure 3.
Figure 3 The omit (2F[o]-F[c]) electron density map for hexagonal K36E at the N-terminal region. The map was calculated by omitting residues 10 -24 in both of the Fis homodimer subunits in the hexagonal asymmetric unit. Simulated annealing refinement was done with a 3 spherical shell of fixed atoms surrounding the omitted regions, and the maps were contoured at 1.0 of the average electron density.
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1997, 16, 6860-6873) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20140235 J.A.Steen, J.A.Steen, P.Harrison, T.Seemann, I.Wilkie, M.Harper, B.Adler, and J.D.Boyce (2010).
Fis is essential for capsule production in Pasteurella multocida and regulates expression of other important virulence factors.
  PLoS Pathog, 6, e1000750.  
20395367 S.Stella, D.Cascio, and R.C.Johnson (2010).
The shape of the DNA minor groove directs binding by the DNA-bending protein Fis.
  Genes Dev, 24, 814-826.
PDB codes: 3iv5 3jr9 3jra 3jrb 3jrc 3jrd 3jre 3jrf 3jrg 3jrh 3jri
19560425 G.Dhar, J.K.Heiss, and R.C.Johnson (2009).
Mechanical constraints on Hin subunit rotation imposed by the Fis/enhancer system and DNA supercoiling during site-specific recombination.
  Mol Cell, 34, 746-759.  
18178221 Y.Shao, L.S.Feldman-Cohen, and R.Osuna (2008).
Functional characterization of the Escherichia coli Fis-DNA binding sequence.
  J Mol Biol, 376, 771-785.  
18514225 Y.Shao, L.S.Feldman-Cohen, and R.Osuna (2008).
Biochemical identification of base and phosphate contacts between Fis and a high-affinity DNA binding site.
  J Mol Biol, 380, 327-339.  
17275024 C.V.Papagiannis, M.D.Sam, M.A.Abbani, D.Yoo, D.Cascio, R.T.Clubb, and R.C.Johnson (2007).
Fis targets assembly of the Xis nucleoprotein filament to promote excisive recombination by phage lambda.
  J Mol Biol, 367, 328-343.
PDB code: 2og0
17045294 D.Skoko, D.Yoo, H.Bai, B.Schnurr, J.Yan, S.M.McLeod, J.F.Marko, and R.C.Johnson (2006).
Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein Fis.
  J Mol Biol, 364, 777-798.  
16513738 L.S.Feldman-Cohen, Y.Shao, D.Meinhold, C.Miller, W.Colón, and R.Osuna (2006).
Common and variable contributions of Fis residues to high-affinity binding at different DNA sequences.
  J Bacteriol, 188, 2081-2095.  
16756503 N.D.Grindley, K.L.Whiteson, and P.A.Rice (2006).
Mechanisms of site-specific recombination.
  Annu Rev Biochem, 75, 567-605.  
15368583 J.Zhang, Y.Zeuner, A.Kleefeld, G.Unden, and A.Janshoff (2004).
Multiple site-specific binding of Fis protein to Escherichia coli nuoA-N promoter DNA and its impact on DNA topology visualised by means of scanning force microscopy.
  Chembiochem, 5, 1286-1289.  
14763986 S.K.Merickel, and R.C.Johnson (2004).
Topological analysis of Hin-catalysed DNA recombination in vivo and in vitro.
  Mol Microbiol, 51, 1143-1154.  
15208307 X.F.Yang, Y.Ji, B.L.Schneider, and L.Reitzer (2004).
Phosphorylation-independent dimer-dimer interactions by the enhancer-binding activator NtrC of Escherichia coli: a third function for the C-terminal domain.
  J Biol Chem, 279, 36708-36714.  
13679374 H.Zhi, X.Wang, J.E.Cabrera, R.C.Johnson, and D.J.Jin (2003).
Fis stabilizes the interaction between RNA polymerase and the ribosomal promoter rrnB P1, leading to transcriptional activation.
  J Biol Chem, 278, 47340-47349.  
12885629 J.Huang, Q.Zhang, and T.Schlick (2003).
Effect of DNA superhelicity and bound proteins on mechanistic aspects of the Hin-mediated and Fis-enhanced inversion.
  Biophys J, 85, 804-817.  
12235381 P.Ray, K.J.Smith, R.A.Parslow, R.Dixon, and E.I.Hyde (2002).
Secondary structure and DNA binding by the C-terminal domain of the transcriptional activator NifA from Klebsiella pneumoniae.
  Nucleic Acids Res, 30, 3972-3980.  
12070319 S.A.Hobart, S.Ilin, D.F.Moriarty, R.Osuna, and W.Colón (2002).
Equilibrium denaturation studies of the Escherichia coli factor for inversion stimulation: implications for in vivo function.
  Protein Sci, 11, 1671-1680.  
10064606 P.H.Arnold, D.G.Blake, N.D.Grindley, M.R.Boocock, and W.M.Stark (1999).
Mutants of Tn3 resolvase which do not require accessory binding sites for recombination activity.
  EMBO J, 18, 1407-1414.  
10594822 S.G.Smith, and C.J.Dorman (1999).
Functional analysis of the FimE integrase of Escherichia coli K-12: isolation of mutant derivatives with altered DNA inversion preferences.
  Mol Microbiol, 34, 965-979.  
10465734 W.S.Tzou, and M.J.Hwang (1999).
Modeling helix-turn-helix protein-induced DNA bending with knowledge-based distance restraints.
  Biophys J, 77, 1191-1205.  
  9761468 A.Rajpal, M.G.Taylor, and J.F.Kirsch (1998).
Quantitative evaluation of the chicken lysozyme epitope in the HyHEL-10 Fab complex: free energies and kinetics.
  Protein Sci, 7, 1868-1874.  
9628859 M.A.Schumacher, D.Carter, D.M.Scott, D.S.Roos, B.Ullman, and R.G.Brennan (1998).
Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding.
  EMBO J, 17, 3219-3232.
PDB codes: 1bd3 1bd4 1upf 1upu
  9732277 S.K.Merickel, M.J.Haykinson, and R.C.Johnson (1998).
Communication between Hin recombinase and Fis regulatory subunits during coordinate activation of Hin-catalyzed site-specific DNA inversion.
  Genes Dev, 12, 2803-2816.  
  9811654 S.Y.Lee, H.J.Lee, H.Lee, S.Kim, E.H.Cho, and H.M.Lim (1998).
In vivo assay of protein-protein interactions in Hin-mediated DNA inversion.
  J Bacteriol, 180, 5954-5960.  
  9761469 W.Z.Yang, T.P.Ko, L.Corselli, R.C.Johnson, and H.S.Yuan (1998).
Conversion of a beta-strand to an alpha-helix induced by a single-site mutation observed in the crystal structure of Fis mutant Pro26Ala.
  Protein Sci, 7, 1875-1883.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.