Zinc Finger Motif by yurtgc548

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									Zinc Finger Motif


   Eylem Aydogdu
      03/28/08
           Zinc Finger Motif
• The zinc finger is a
  ~26 amino acid
  (not nucleotide)
  residue peptide
  that forms a
  structure which
  binds to specific
  sequences in DNA.
  The consensus sequence of the Zinc Finger
1. C2-H2 zinc finger:
• Cys-X2-5-Cys-X12-His-X3-6-His [1]
• Cys-X2-4-Cys-X3-Phe-X5-Leu-X2-His-X3-His [2]

2. C4 zinc finger:
• Cys-X2-Cys-X13-Cys-X2-Cys-X14-15-Cys-X5-Cys-X9-Cys-X2-Cys

3. C6 zinc finger:
• C-X2-C-X6-C-X5-6-C-X2-C-X6-C

1. Atomic Contact To Cellular Function By Shiro Iuchi, Natalie Kuldell
2. Hiroshi Takatsujiठand Takashi Matsumoto.1996.THE JOURNAL OF BIOLOGICAL CHEMISTRY.
 How to convert an amino acid sequence into
          a nucleotide sequence?
• Zinc finger is an amino acid (aa) sequence
  which makes a protein.
• There are 20 common aa which makes the
  proteins.
    G - Glycine (Gly)         W - Tryptophan (Trp)
    P - Proline (Pro)         H - Histidine (His)
    A - Alanine (Ala)         K - Lysine (Lys)
    V - Valine (Val)          R - Arginine (Arg)
    L - Leucine (Leu)         Q - Glutamine (Gln)
    I - Isoleucine (Ile)      N - Asparagine (Asn)
    M - Methionine (Met)      E - Glutamic Acid (Glu)
    C - Cysteine (Cys)        D - Aspartic Acid (Asp)
    F - Phenylalanine (Phe)   S - Serine (Ser)
    Y - Tyrosine (Tyr)        T - Threonine (Thr)
How to convert an amino acid sequence into
         a nucleotide sequence?
• Each aa is encoded by 3 nucleotides. (Every 3
  nucleotides in coding region of DNA represents
  1 aa in a protein chain.)
• We can convert an aa sequence into a
  nucleotide sequence by replacing the aa with its
  specific 3 nucleotide codon.
• Exp.: 3 nucleotide codon for His is: CAT or CAC
                               Cys : TGT or TGC
DNA Codon Table
How to convert an amino acid sequence into
         a nucleotide sequence?
An example of two complementary strands of DNA would
   be:
5‘-ATGGAATTCTCGCTC-3' (Coding, sense strand)

3‘-TACCTTAAGAGCGAG-5’ (Template, antisense strand)

5'-AUGGAAUUCUCGCUC-3'(mRNA made from Template)

• Since amino acid residues of proteins are specified as
  triplet codons, the protein sequence made from the
  above example would be;
• Met-Glu-Phe-Ser-Leu (MEFSL).
   Notation sheet for next slide
X= any amino acid
X2-5= number of Xs varies between 2 and 5
N= any nucleotide
N6/9/12= number of Ns can be 6 OR 9 OR 12

T-G-T/C
1 2 3 3= these numbers indicates the index of the
  nucleotide sequence.
           Zinc Finger Pattern
• Amino acid seq.:
  Cys-X2-5-Cys-X12-His-X3-6-His

Cys: TGC or TGT , His: CAT or CAC

• Nucleotide seq.:
  T-G-T/C-N6/9/12/15-T-G-T/C-N36-C-A-T/C-N9/12/15/18-
  1 2 3 3…N……...1 2 3 3..N…1 2 3 3…..N……
  C-A-T/C
  1 2 33
               Attention!
• Pattern search must be initialized from the
  start codon of a gene (keep sequence in
  frame). Random start positions may result
  in wrong aa coding because each aa
  made of 3 nucleotides and any shift in any
  direction will generate nonsense aa
  sequence.

								
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