Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase.
Eubacterial leucyl/phenylalanyl-tRNA protein transferase (LF-transferase) catalyses peptide-bond formation by using Leu-tRNA(Leu) (or Phe-tRNA(Phe)) and an amino-terminal Arg (or Lys) of a protein, as donor and acceptor substrates, respectively. However, the catalytic mechanism of peptide-bond formation by LF-transferase remained obscure. Here we determine the structures of complexes of LF-transferase and phenylalanyl adenosine, with and without a short peptide bearing an N-terminal Arg. Combining the two separate structures into one structure as well as mutation studies reveal the mechanism for peptide-bond formation by LF-transferase. The electron relay from Asp 186 to Gln 188 helps Gln 188 to attract a proton from the alpha-amino group of the N-terminal Arg of the acceptor peptide. This generates the attacking nucleophile for the carbonyl carbon of the aminoacyl bond of the aminoacyl-tRNA, thus facilitating peptide-bond formation. The protein-based mechanism for peptide-bond formation by LF-transferase is similar to the reverse reaction of the acylation step observed in the peptide hydrolysis reaction by serine proteases.
Watanabe
Kazunori
K
Institute of Biological Resources and Functions, National Institute of Advanced Industrial Sciences and Technology, 1-1-1, Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan.
Toh
Yukimatsu
Y
Suto
Kyoko
K
Shimizu
Yoshihiro
Y
Oka
Natsuhisa
N
Wada
Takeshi
T
Tomita
Kozo
K
D000215:Acylation; D000241:Adenosine / Q000031:analogs & derivatives / Q000378:metabolism; D000595:Amino Acid Sequence; D001665:Binding Sites; D002364:Caseins / Q000096:biosynthesis / Q000737:chemistry; D002384:Catalysis; D004926:Escherichia coli / Q000201:enzymology*; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008958:Models, Molecular; D010446:Peptide Fragments / Q000096:biosynthesis* / Q000737:chemistry*; D010458:Peptidyl Transferases / Q000737:chemistry* / Q000378:metabolism*; D010649:Phenylalanine / Q000378:metabolism; D010652:Phenylalanine-tRNA Ligase / Q000378:metabolism; D014176:Protein Biosynthesis; D011487:Protein Conformation; D011691:Puromycin / Q000737:chemistry / Q000378:metabolism; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry / Q000378:metabolism*; D013379:Substrate Specificity
D002364:Caseins; D010446:Peptide Fragments; D012346:RNA, Transfer, Amino Acyl; D010649:Phenylalanine; D011691:Puromycin; D010458:Peptidyl Transferases; D010652:Phenylalanine-tRNA Ligase; D000241:Adenosine