2Z3L
complex structure of LF-transferase and peptide A
Summary for 2Z3L
| Entry DOI | 10.2210/pdb2z3l/pdb |
| Related | 2Z3K 2Z3M 2Z3N 2Z3O 2Z3P |
| Descriptor | Leucyl/phenylalanyl-tRNA-protein transferase, peptide (PHE)(ARG)(TYR)(LEU)(GLY), D(-)-TARTARIC ACID, ... (4 entities in total) |
| Functional Keywords | lf-transferase, transferase |
| Biological source | Escherichia coli More |
| Cellular location | Cytoplasm: P0A8P1 |
| Total number of polymer chains | 4 |
| Total formula weight | 54652.34 |
| 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 Cited by 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: 17891155DOI: 10.1038/nature06167 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.75 Å) |
Structure validation
Download full validation report
