Lac repressor

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Challenge Your Understanding

Here are some questions to challenge your understanding.

  1. Why does the lac repressor bind to DNA non-specifically?
  2. When the lac repressor binds non-specifically to DNA, what part of the DNA double helix does it bind to?
  3. Does DNA have a net charge, and if so, is it negative or positive in aqueous solution at pH 7?
  4. What kinds of chemical bonds are likely to be involved in non-specific binding of the repressor protein to DNA?
  5. Does specific binding of lac repressor to DNA disrupt any of the Watson-Crick hydrogen bonds between the base pairs in the DNA strands?
  6. How do proteins such as the lac repressor recognize specific nucleotide sequences in a DNA double helix?
  7. What kinds of chemical bonds are involved in specific binding of the repressor protein to DNA?
  8. Does the lac repressor recognize specific bases in the major or minor grooves of the DNA?
  9. When it recognizes its specific nucleotide sequence, how does the lac repressor stabilize a kink in the DNA double helix?

Answers are available on request to Image:Contact-email.png. If you would like us to make the answers publically available within Proteopedia, please let us know. When contacting us, please give your full name, your position, institution or school, and location.


Content Attribution & Acknowledgement

The morphs displayed here were originally prepared by Eric Martz in 2004 for the page Lac Repressor Binding to DNA, within ProteinExplorer.Org.

Eric Martz thanks Remo Rohs for his kind and expert advice concerning the 2010-2011 updates to this article.

3D structures of Lac repressor

Lac repressor 3D structures

See Also


References & Notes

  1. L'opéron: groupe de gènes à expression coordonée par un opérateur. [Operon: a group of genes with the expression coordinated by an operator.] C R Hebd Seances Acad Sci., 250:1727-9, 1960. PubMed 14406329
  2. The lac repressor. Lewis, M. C R Biol. 328:521-48, 2005. PubMed 15950160
  3. This domain coloring scheme is adapted from Fig. 6 in the review by Lewis (C. R. Biol. 328:521, 2005). Domains are 1-45, 46-62, (63-162,291-320), (163-290,321-332), 330-339, and 340-357.
  4. Conservation results for 1lbg are from the precalculated ConSurf Database, using 103 sequences from Swiss-Prot with an average pairwise distance of 2.4.
  5. Conservation results for 1lbi are from the ConSurf Server, using 100 sequences from Uniprot with an average pairwise distance of 1.3.
  6. 6.0 6.1 For these scenes, the 20-model PDB files for 1osl and 1l1m were reduced in size, to avoid exceeding the java memory available to the Jmol applet. All atoms except amino acid alpha carbons and DNA phosphorus atoms were removed using the free program alphac.exe from PDBTools. Secondary structure HELIX records from the original PDB file header were retained. The results are Image:1osl ca.pdb and Image:1l1m ca.pdb.
  7. Hammar P, Leroy P, Mahmutovic A, Marklund EG, Berg OG, Elf J. The lac repressor displays facilitated diffusion in living cells. Science. 2012 Jun 22;336(6088):1595-8. PMID:22723426 doi:10.1126/science.1221648
  8. 8.0 8.1 8.2 8.3 8.4 8.5 8.6 Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS. Origins of specificity in protein-DNA recognition. Annu Rev Biochem. 2010;79:233-69. PMID:20334529 doi:10.1146/annurev-biochem-060408-091030
  9. Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS. Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell. 2007 Nov 2;131(3):530-43. PMID:17981120 doi:10.1016/j.cell.2007.09.024
  10. 10.0 10.1 10.2 Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B. The role of DNA shape in protein-DNA recognition. Nature. 2009 Oct 29;461(7268):1248-53. PMID:19865164 doi:10.1038/nature08473
  11. Nikolova EN, Kim E, Wise AA, O'Brien PJ, Andricioaei I, Al-Hashimi HM. Transient Hoogsteen base pairs in canonical duplex DNA. Nature. 2011 Feb 24;470(7335):498-502. Epub 2011 Jan 26. PMID:21270796 doi:10.1038/nature09775
  12. Honig B, Rohs R. Biophysics: Flipping Watson and Crick. Nature. 2011 Feb 24;470(7335):472-3. PMID:21350476 doi:10.1038/470472a
  13. Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z. Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nat Struct Mol Biol. 2010 Apr;17(4):423-9. Epub 2010 Apr 4. PMID:20364130 doi:10.1038/nsmb.1800
  14. Powerpoint is a registered trademark for a software package licensed by Microsoft Corp..

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Alexander Berchansky, Michal Harel, David Canner, Eran Hodis

DOI: http://dx.doi.org/10.14576/324680.1823276 (?)
Citation: Martz E, Hodis E, Canner D, Harel M, Berchansky A, 2013, "Lac repressor", Proteopedia, DOI: http://dx.doi.org/10.14576/324680.1823276
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