Palindromes in proteins.
Palindromes in DNA consist of nucleotides sequences that read the same from the 5'-end to the 3'-end, and its double helix is related by twofold axis. They occur in genomes of all organisms and have various functions. For example, restriction enzymes often recognize palindromic sequences of DNA. Palindromes in telomeres are crucial for initiation of replication. One can ask the questions, Do palindromes occur in protein, and if so, what function they play? We have searched the protein SWISSPROT database for palindromic sequences. A great number (26%) of different protein palindromes were found. One example of such protein is systemin, an 18-amino-acid-long peptide. It contains palindrome in its beta-sheet domain that interacts with palindromic fragment of DNA. The other palindrome containing protein is cellular human tumor suppressor p53. Oligonucleotide LTI-ITL has been observed in the crystal structure and is located close to a DNA recognizing domain. As the number of possible palindromic sequences of a given length is far much greater for proteins (20N) than for nucleic acids (4N), the study on their role seems to be an exciting challenge. Our results have clearly showed that palindromes are frequently occurring motives in proteins. Moreover, even very few examples that we have examined so far indicate the importance of further studies on protein palindromes.
Giel-Pietraszuk
Malgorzata
M
Institute for Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Hoffmann
Marcin
M
Dolecka
Sylwia
S
Rychlewski
Jacek
J
Barciszewski
Jan
J
D000595:Amino Acid Sequence; D003461:Crystallography; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D003627:Data Interpretation, Statistical; D016208:Databases, Factual; D006801:Humans; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000737:chemistry* / Q000235:genetics*; D010455:Peptides / Q000737:chemistry* / Q000235:genetics*; D010727:Phosphoric Diester Hydrolases / Q000737:chemistry / Q000235:genetics; D011116:Polynucleotide 5'-Hydroxyl-Kinase / Q000737:chemistry / Q000235:genetics; D011118:Polynucleotide Ligases / Q000737:chemistry / Q000235:genetics; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D013329:Structure-Activity Relationship; D016159:Tumor Suppressor Protein p53 / Q000737:chemistry / Q000235:genetics
D004279:DNA, Viral; D009841:Oligonucleotides; D010455:Peptides; D011506:Proteins; D016159:Tumor Suppressor Protein p53; C059150:tRNA ligase, yeast; C073704:systemin; D011116:Polynucleotide 5'-Hydroxyl-Kinase; D010727:Phosphoric Diester Hydrolases; D011118:Polynucleotide Ligases