2Z3P

complex structure of LF-transferase and leucine

Summary for 2Z3P

• Entry DOI: 10.2210/pdb2z3p/pdb
• Related: 2Z3K 2Z3L 2Z3M 2Z3N 2Z3O
• Descriptor: Leucyl/phenylalanyl-tRNA-protein transferase, LEUCINE, D(-)-TARTARIC ACID, ... (4 entities in total)
• Functional Keywords: lf-transferase, transferase
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P0A8P1
• Total number of polymer chains: 2
• Total formula weight: 53603.16

Authors

Watanabe, K.,Toh, Y.,Tomita, K. (deposition date: 2007-06-04, release date: 2007-10-23, Last modification date: 2023-11-01)

Primary citation

Watanabe, K.,Toh, Y.,Suto, K.,Shimizu, Y.,Oka, N.,Wada, T.,Tomita, K.
Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase
Nature, 449:867-871, 2007

PubMed Abstract: 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.

PubMed: 17891155
DOI: 10.1038/nature06167

Experimental method

X-RAY DIFFRACTION (2.5 Å)