There are several different families of proteins containing this particular DNA binding motif. This section deals with two proteins having Zinc finger motifs.
TRANSCRIPTION FACTOR IIIA TFIIA is a transcription factor. The protein contains a repeated motif of roughly 30 amino acid residues. This sequence is repeated 9 times in this protein. Cys and His residues are favoured for Zn binding and the conformation of the zinc fingers is such that these sidechains are oriented optimally for Zn binding. The protein has NO activity as a transcription factor without the zinc bound. There is good evidence that zinc binds to the protein and it is also known that the protein is inactive as a transcription factor unless zinc is bound. Note from the structure that there is a helix associated with the zinc finger. It is this helix which is involved in DNA binding, usually into the major groove. Most DNA binding proteins have a recognition. The different motifs essentially are different methods for supporting and orienting the recognition helix. (eg helix - loop - helix) OTHER ZN FINGERS Zn268 is a protein which contains three zinc fingers. Note that each zinc finger has a helix associated with it and it is the helix which is involved in binding to the recognition sequence on the DNA. The structure of the Zn-Fingers are identical. , and consist of a b-hairpin followed by an a-helix. These are held in place by the zinc atom. Note the yellow cysteine and mauve histidine sidechains. The protein recognises a 9 base DNA sequence... but it only interacts with one strand of DNA, unlike many other DNA binding proteins. It does not form a dimer, and the target sequence is not rotationally symmetrical. The sequence is guanine rich, although this is not necessary for all Zn fingers. Each finger recognises three bases on the strand... The helices of the fingers, fit into the major groove of the DNA, with the N-terminal ends interacting with the phosphate backbone. Recognition derives from the specific H-bonds from the Arginine residues in the protein to the guanine bases in the DNA. There is no distortion of the DNA when the protein binds. The fingers simply slot into the major groove. Compare this to CAP which is rigid, forcing the DNA to bend, and adapt. The Zinc fingers are inherently flexible, and they adapt to the DNA structure instead. This leads to the suggestion that different proteins may be used for different purposes, i.e. if distortion is desired, a rigid protein will be used. If it is not necessary, then perhaps a more flexible protein will suffice. There is only one more motif involved in DNA binding proteins, and it is are dealt with in the penultimate tutorial. Press NEXT to view it now, or go HOME if you wish to finish for the day.
TFIIA is a transcription factor. The protein contains a repeated motif of roughly 30 amino acid residues. This sequence is repeated 9 times in this protein. Cys and His residues are favoured for Zn binding and the conformation of the zinc fingers is such that these sidechains are oriented optimally for Zn binding. The protein has NO activity as a transcription factor without the zinc bound. There is good evidence that zinc binds to the protein and it is also known that the protein is inactive as a transcription factor unless zinc is bound. Note from the structure that there is a helix associated with the zinc finger. It is this helix which is involved in DNA binding, usually into the major groove. Most DNA binding proteins have a recognition. The different motifs essentially are different methods for supporting and orienting the recognition helix. (eg helix - loop - helix) OTHER ZN FINGERS Zn268 is a protein which contains three zinc fingers. Note that each zinc finger has a helix associated with it and it is the helix which is involved in binding to the recognition sequence on the DNA. The structure of the Zn-Fingers are identical. , and consist of a b-hairpin followed by an a-helix. These are held in place by the zinc atom. Note the yellow cysteine and mauve histidine sidechains. The protein recognises a 9 base DNA sequence... but it only interacts with one strand of DNA, unlike many other DNA binding proteins. It does not form a dimer, and the target sequence is not rotationally symmetrical. The sequence is guanine rich, although this is not necessary for all Zn fingers. Each finger recognises three bases on the strand... The helices of the fingers, fit into the major groove of the DNA, with the N-terminal ends interacting with the phosphate backbone. Recognition derives from the specific H-bonds from the Arginine residues in the protein to the guanine bases in the DNA. There is no distortion of the DNA when the protein binds. The fingers simply slot into the major groove. Compare this to CAP which is rigid, forcing the DNA to bend, and adapt. The Zinc fingers are inherently flexible, and they adapt to the DNA structure instead. This leads to the suggestion that different proteins may be used for different purposes, i.e. if distortion is desired, a rigid protein will be used. If it is not necessary, then perhaps a more flexible protein will suffice. There is only one more motif involved in DNA binding proteins, and it is are dealt with in the penultimate tutorial. Press NEXT to view it now, or go HOME if you wish to finish for the day.
Cys and His residues are favoured for Zn binding and the conformation of the zinc fingers is such that these sidechains are oriented optimally for Zn binding. The protein has NO activity as a transcription factor without the zinc bound.
OTHER ZN FINGERS Zn268 is a protein which contains three zinc fingers. Note that each zinc finger has a helix associated with it and it is the helix which is involved in binding to the recognition sequence on the DNA. The structure of the Zn-Fingers are identical. , and consist of a b-hairpin followed by an a-helix. These are held in place by the zinc atom. Note the yellow cysteine and mauve histidine sidechains. The protein recognises a 9 base DNA sequence... but it only interacts with one strand of DNA, unlike many other DNA binding proteins. It does not form a dimer, and the target sequence is not rotationally symmetrical. The sequence is guanine rich, although this is not necessary for all Zn fingers. Each finger recognises three bases on the strand... The helices of the fingers, fit into the major groove of the DNA, with the N-terminal ends interacting with the phosphate backbone. Recognition derives from the specific H-bonds from the Arginine residues in the protein to the guanine bases in the DNA. There is no distortion of the DNA when the protein binds. The fingers simply slot into the major groove. Compare this to CAP which is rigid, forcing the DNA to bend, and adapt. The Zinc fingers are inherently flexible, and they adapt to the DNA structure instead. This leads to the suggestion that different proteins may be used for different purposes, i.e. if distortion is desired, a rigid protein will be used. If it is not necessary, then perhaps a more flexible protein will suffice. There is only one more motif involved in DNA binding proteins, and it is are dealt with in the penultimate tutorial. Press NEXT to view it now, or go HOME if you wish to finish for the day.
Zn268 is a protein which contains three zinc fingers. Note that each zinc finger has a helix associated with it and it is the helix which is involved in binding to the recognition sequence on the DNA. The structure of the Zn-Fingers are identical. , and consist of a b-hairpin followed by an a-helix. These are held in place by the zinc atom. Note the yellow cysteine and mauve histidine sidechains. The protein recognises a 9 base DNA sequence... but it only interacts with one strand of DNA, unlike many other DNA binding proteins. It does not form a dimer, and the target sequence is not rotationally symmetrical. The sequence is guanine rich, although this is not necessary for all Zn fingers. Each finger recognises three bases on the strand... The helices of the fingers, fit into the major groove of the DNA, with the N-terminal ends interacting with the phosphate backbone. Recognition derives from the specific H-bonds from the Arginine residues in the protein to the guanine bases in the DNA. There is no distortion of the DNA when the protein binds. The fingers simply slot into the major groove. Compare this to CAP which is rigid, forcing the DNA to bend, and adapt. The Zinc fingers are inherently flexible, and they adapt to the DNA structure instead. This leads to the suggestion that different proteins may be used for different purposes, i.e. if distortion is desired, a rigid protein will be used. If it is not necessary, then perhaps a more flexible protein will suffice. There is only one more motif involved in DNA binding proteins, and it is are dealt with in the penultimate tutorial. Press NEXT to view it now, or go HOME if you wish to finish for the day.
Note that each zinc finger has a helix associated with it and it is the helix which is involved in binding to the recognition sequence on the DNA.
The structure of the Zn-Fingers are identical. , and consist of a b-hairpin followed by an a-helix. These are held in place by the zinc atom. Note the yellow cysteine and mauve histidine sidechains. The protein recognises a 9 base DNA sequence... but it only interacts with one strand of DNA, unlike many other DNA binding proteins. It does not form a dimer, and the target sequence is not rotationally symmetrical. The sequence is guanine rich, although this is not necessary for all Zn fingers. Each finger recognises three bases on the strand... The helices of the fingers, fit into the major groove of the DNA, with the N-terminal ends interacting with the phosphate backbone. Recognition derives from the specific H-bonds from the Arginine residues in the protein to the guanine bases in the DNA. There is no distortion of the DNA when the protein binds. The fingers simply slot into the major groove. Compare this to CAP which is rigid, forcing the DNA to bend, and adapt. The Zinc fingers are inherently flexible, and they adapt to the DNA structure instead. This leads to the suggestion that different proteins may be used for different purposes, i.e. if distortion is desired, a rigid protein will be used. If it is not necessary, then perhaps a more flexible protein will suffice. There is only one more motif involved in DNA binding proteins, and it is are dealt with in the penultimate tutorial. Press NEXT to view it now, or go HOME if you wish to finish for the day.
The protein recognises a 9 base DNA sequence...
The sequence is guanine rich, although this is not necessary for all Zn fingers. Each finger recognises three bases on the strand...
The helices of the fingers, fit into the major groove of the DNA, with the N-terminal ends interacting with the phosphate backbone. Recognition derives from the specific H-bonds from the Arginine residues in the protein to the guanine bases in the DNA. There is no distortion of the DNA when the protein binds. The fingers simply slot into the major groove. Compare this to CAP which is rigid, forcing the DNA to bend, and adapt. The Zinc fingers are inherently flexible, and they adapt to the DNA structure instead. This leads to the suggestion that different proteins may be used for different purposes, i.e. if distortion is desired, a rigid protein will be used. If it is not necessary, then perhaps a more flexible protein will suffice. There is only one more motif involved in DNA binding proteins, and it is are dealt with in the penultimate tutorial. Press NEXT to view it now, or go HOME if you wish to finish for the day.
There is no distortion of the DNA when the protein binds. The fingers simply slot into the major groove. Compare this to CAP which is rigid, forcing the DNA to bend, and adapt. The Zinc fingers are inherently flexible, and they adapt to the DNA structure instead.
This leads to the suggestion that different proteins may be used for different purposes, i.e. if distortion is desired, a rigid protein will be used. If it is not necessary, then perhaps a more flexible protein will suffice.
There is only one more motif involved in DNA binding proteins, and it is are dealt with in the penultimate tutorial. Press NEXT to view it now, or go HOME if you wish to finish for the day.
