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  • Cys-X2-4-Cys-X3-Phe-X5-Leu-X2-His-X3-His  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 Takatsuji‡§ and 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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