PDBsum entry 1p7a

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protein metals links
DNA binding protein PDB id
Protein chain
37 a.a. *
* Residue conservation analysis
PDB id:
Name: DNA binding protein
Title: Solution stucture of the third zinc finger from bklf
Structure: Kruppel-like factor 3. Chain: a. Fragment: residues 9-37. Synonym: bf3, bklf. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Gene: bklf. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 20 models
Authors: R.J.Y.Simpson,E.D.Cram,R.Czolij,J.M.Matthews,M.Crossley, J.P.Mackay
Key ref:
R.J.Simpson et al. (2003). CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions. J Biol Chem, 278, 28011-28018. PubMed id: 12736264 DOI: 10.1074/jbc.M211146200
30-Apr-03     Release date:   30-Dec-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q60980  (KLF3_MOUSE) -  Krueppel-like factor 3
344 a.a.
37 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     2 terms  


DOI no: 10.1074/jbc.M211146200 J Biol Chem 278:28011-28018 (2003)
PubMed id: 12736264  
CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions.
R.J.Simpson, E.D.Cram, R.Czolij, J.M.Matthews, M.Crossley, J.P.Mackay.
Classical (CCHH) zinc fingers are among the most common protein domains found in eukaryotes. They function as molecular recognition elements that mediate specific contact with DNA, RNA, or other proteins and are composed of a betabetaalpha fold surrounding a single zinc ion that is ligated by two cysteine and two histidine residues. In a number of variant zinc fingers, the final histidine is not conserved, and in other unrelated zinc binding domains, residues such as aspartate can function as zinc ligands. To test whether the final histidine is required for normal folding and the DNA-binding function of classical zinc fingers, we focused on finger 3 of basic Krüppel-like factor. The structure of this domain was determined using NMR spectroscopy and found to constitute a typical classical zinc finger. We generated a panel of substitution mutants at the final histidine in this finger and found that several of the mutants retained some ability to fold in the presence of zinc. Consistent with this result, we showed that mutation of the final histidine had only a modest effect on DNA binding in the context of the full three-finger DNA-binding domain of basic Krüppel-like factor. Further, the zinc binding ability of one of the point mutants was tested and found to be indistinguishable from the wild-type domain. These results suggest that the final zinc chelating histidine is not an essential feature of classical zinc fingers and have implications for zinc finger evolution, regulation, and the design of experiments testing the functional roles of these domains.
  Selected figure(s)  
Figure 3.
FIG. 3. Solution structure of BF3. A, ensemble of the best 25 structures of BF3. Structures are superimposed over the backbone atoms of residues 319-342 (the N-terminal eight, which are unstructured, are omitted for clarity). The zinc-chelating side chains are shown in orange, and the zinc atom is shown in gray. B, ribbon diagram of the lowest energy structure of BF3, showing elements of secondary structure as recognized in the program MOLMOL (30). C, overlay over the backbone atoms (Ca, C', N, Cys321-His341 of BF3) of BF3 with the second zinc finger of Zif268 (45). BF3 is shown in blue, and Zif268-F2 is shown in red.
Figure 5.
FIG. 5. BF3E is monomeric in solution. Sedimentation equilibrium data for BF3E recorded at 42,000 rpm (25 °C). The lower graph displays a plot of absorbance at 230 nm versus r2/2 (cm2), whereas the upper graph illustrates the residual deviations resulting from the fit of an ideal single species model to the data.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 28011-28018) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20607778 M.Imanishi, T.Nakaya, T.Morisaki, D.Noshiro, S.Futaki, and Y.Sugiura (2010).
Metal-stimulated regulation of transcription by an artificial zinc-finger protein.
  Chembiochem, 11, 1653-1655.  
19416940 H.R.Kim, K.S.Chae, K.H.Han, and D.M.Han (2009).
The nsdC gene encoding a putative C2H2-type transcription factor is a key activator of sexual development in Aspergillus nidulans.
  Genetics, 182, 771-783.  
19369210 I.Baglivo, L.Russo, S.Esposito, G.Malgieri, M.Renda, A.Salluzzo, B.Di Blasio, C.Isernia, R.Fattorusso, and P.V.Pedone (2009).
The structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains.
  Proc Natl Acad Sci U S A, 106, 6933-6938.  
16382145 W.Zhang, B.Li, R.Singh, U.Narendra, L.Zhu, and M.A.Weiss (2006).
Regulation of sexual dimorphism: mutational and chemogenetic analysis of the doublesex DM domain.
  Mol Cell Biol, 26, 535-547.  
15644435 C.K.Liew, R.J.Simpson, A.H.Kwan, L.A.Crofts, F.E.Loughlin, J.M.Matthews, M.Crossley, and J.P.Mackay (2005).
Zinc fingers as protein recognition motifs: structural basis for the GATA-1/friend of GATA interaction.
  Proc Natl Acad Sci U S A, 102, 583-588.
PDB code: 1y0j
15020707 A.Kozaki, S.Hake, and J.Colasanti (2004).
The maize ID1 flowering time regulator is a zinc finger protein with novel DNA binding properties.
  Nucleic Acids Res, 32, 1710-1720.  
15169884 A.L.Nielsen, P.Jørgensen, T.Lerouge, M.Cerviño, P.Chambon, and R.Losson (2004).
Nizp1, a novel multitype zinc finger protein that interacts with the NSD1 histone lysine methyltransferase through a unique C2HR motif.
  Mol Cell Biol, 24, 5184-5196.  
15542849 X.Chen, and J.J.Bieker (2004).
Stage-specific repression by the EKLF transcriptional activator.
  Mol Cell Biol, 24, 10416-10424.  
14530457 A.H.Kwan, R.Czolij, J.P.Mackay, and M.Crossley (2003).
Pentaprobe: a comprehensive sequence for the one-step detection of DNA-binding activities.
  Nucleic Acids Res, 31, e124.  
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 code is shown on the right.