Lambda Repressor: 2HNF

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Lambda Repressor 2HNF

• Amber Sanders
• Brad Weaver
• Jacob Hicks

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Background Info

• Amber Sanders

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General information about Lambda Repressor

• Generally found in vertebrates and E.coli
• Is best studied in E.coli
• Crystallized as monomer using X-ray diffraction

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Lambda repressor and E.coli

• Lambda repressor and the SOS response
• Assists in the DNA repair mechanism
• Determines whether the cell is lysogenic or lytic

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http//gibk26.bse.kyutech.ac.jp/jouhou/image/dna-p
rotein/all/all.html
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Lambda repressor mechanism in E.coli
http//www.biochem.arizona.edu/classes/bioc471/pag
es/Lecture5/Lecture5.html
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Energy
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Applications

• Gene manipulation or gene therapy
• Coumermycin
• Novobiocin

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Structure

• Brad Weaver

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PDB 2HNF

• x-ray diffraction was the method used to
  determine these figures

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Subunits/chains

• Chain A has 130 residues excluding the gaps
• Made up of amino acids

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Gap
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Subunits/chains

• Number of Strands 11
• Number of Helices 0

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Biology Workbench
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Alpha Helices

• PELE showed there is only 1 alpha
• helice, however according to the X-RAY
• diffraction model it has no alpha helices.

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Transmembrane

• TMAP and Grease Results
• NO TRANSMEMBRANE SEGMENTS PREDICTED.

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Disulfide Bond
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Calcium Ligands
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Closer look at the Ligands
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Active Sites

• No active sites, because it is not an enzyme, it
  just has the normal binding sites of a protein

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Motiffs

• N-glycosylation site
• cAMP- and cGMP-dependent protein kinase
  phosphorylation site
• Protein kinase C phosphorylation site
• Casein kinase II phosphorylation site
• N-myristoylation site
• Typical sites of a protein no catalytic site
  because it is not an enzyme.

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Close Families

• Repressor LexA serine protease

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Phylogeny

• Jacob Hicks

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Phylogeny of 2HNF

• Significant Homologs found only within bacterial
  and viral proteins
• All related by regulating gene expression
• Techniques used to determine homology
• Blast search
• Phylogenetic tree
• Multiple sequence alignment

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Phylogenic Tree

• Proteins labeled by species or virus that they
  are found in
• 2HNF found in E. coli
• 1FJR found in Bacteria Phage 186
• Repressor

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Conservation

• Conservation seems heaviest at the end of the
  protein chain
• Other proteins either not monomeric or much
  larger than 2HNF
• Explains the large conservation when 2HNF is
  removed from the alignment

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Conservation of primary structure

• Relatively conserved throughout
• Protein somewhat conserved at the end of the
  sequence
• 2HNF has large terminal gap

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Comparison of 1FJR to 2HNF

• Very little alignment but very similar shape
• Same function
• To bind to DNA

Comparison of segment of 2FJR to 2HNF A
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• 1FJR has two crystallized protein chains
• Much larger structure than complete 2HNF

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References

• Biology Workbench
• Netscape (Protein Explorer)
• Nkjonka,P., Bell,C.E. (2006). Structure of a
  Hyper-cleavable monomeric fragment of phage
  lambda repressor or containing the cleavage site
  region. J.Mol.Biol.362479-489.
• Oobatake,M., Kono,H.,Wang,Y.,Sarai,A. (2003).
  Anatomy of specific interactions between lambda
  repressor and operator DNA. Proteins. 53 (1)
  33-43.
• Zhao,H.F., Boyd,J., Jolicoeur,N.,Shen,S.H.
  (2003). A coumermycin/novobiocin-regulated gene
  expression system. Human Gene Therapy.
  14(17)1619-1629.