138. The PROSITE pattern representing the conserved sequence motif for a new family of AMP binding protein is
[LIVMFY]-X(2)-[STG]-[STAG]-G-[ST]. You are given a sequence of a 15-amino acid stretch starting from the
first residue of the motif. Which one of the following proteins is likely to have AMP binding function?
1. LIVMFYNGSTGSTAG
2. MAGTAGSEGYIRHHC
3. LIVMFYSTGSTAGGS
4. LSSTAYTTSALKAAA

Question

The PROSITE pattern representing the conserved sequence motif for a new family of AMP binding protein is [LIVMFY]-X(2)-[STG]-[STAG]-G-[ST]. You are given a sequence of a 15-amino acid stretch starting from the first residue of the motif. Which one of the following proteins is likely to have AMP binding function?

1. LIVMFYNGSTGSTAG

2. MAGTAGSEGYIRHHC

3. LIVMFYSTGSTAGGS

4. LSSTAYTTSALKAAA

Detailed Explanation

The PROSITE motif you are provided is [LIVMFY]-X(2)-[STG]-[STAG]-G-[ST], which refers to the following sequence pattern:

• [LIVMFY]: The first amino acid must be one of Leucine (L), Isoleucine (I), Valine (V), Methionine (M), Phenylalanine (F), or Tyrosine (Y).

• X(2): The next two amino acids can be any amino acids (denoted by X).

• [STG]: The fourth amino acid must be Serine (S), Threonine (T), or Glycine (G).

• [STAG]: The fifth amino acid must be Serine (S), Threonine (T), Alanine (A), or Glycine (G).

• G: The sixth amino acid must be Glycine (G).

• [ST]: The seventh and final amino acid must be Serine (S) or Threonine (T).

Based on this motif, we will evaluate the provided options:

1. LIVMFYNGSTGSTAG:

   • First amino acid (L) is from [LIVMFY].

   • Second and third amino acids (NG) match the X(2) position (allowing any two amino acids).

   • Fourth amino acid (S) matches [STG].

   • Fifth amino acid (T) matches [STAG].

   • Sixth amino acid (G) is a G, matching the motif.

   • Seventh amino acid (S) matches [ST].

   This sequence matches the PROSITE pattern, so this is a likely candidate for an AMP binding protein.

2. MAGTAGSEGYIRHHC:

   • First amino acid (M) does not match [LIVMFY].

   • The rest of the sequence does not fit the PROSITE pattern.

   • Therefore, this sequence does not correspond to an AMP binding protein.

3. LIVMFYSTGSTAGGS:

   • First amino acid (L) matches [LIVMFY].

   • Second and third amino acids (IV) do not match X(2) (they are valid but part of the next amino acids).

   • The sequence does not perfectly follow the PROSITE motif, particularly at the fourth position where the sequence has T instead of a G in the motif.

4. LSSTAYTTSALKAAA:

   • The first amino acid (L) matches [LIVMFY], but SS does not match the required sequence at positions 2 and 3.

   • This sequence deviates from the PROSITE motif and is unlikely to bind AMP.

Correct Answer: 1. LIVMFYNGSTGSTAG

The sequence LIVMFYNGSTGSTAG closely matches the PROSITE motif [LIVMFY]-X(2)-[STG]-[STAG]-G-[ST], making it the most likely candidate for an AMP binding protein.

Conclusion

Identifying AMP binding proteins using the PROSITE motif involves looking for specific amino acid patterns in the sequence. In this case, the sequence LIVMFYNGSTGSTAG perfectly matches the PROSITE pattern, indicating that this protein is likely to have AMP binding function.