PDBsum entry 2z3l

Transferase

PDB id: 2z3l

Contents

Protein chains

229 a.a. *

Ligands

PHE-ARG-TYR-LEU-GLY ×2

TAR ×2

Waters ×13

* Residue conservation analysis

PDB id:

2z3l

Name:

Transferase

Title:

Complex structure of lf-transferase and peptide a

Structure:

Leucyl/phenylalanyl-tRNA-protein transferase. Chain: a, b. Synonym: aminoacyl-tRNA protein transferase, l/f-transferase, leucyltransferase, phenyalanyltransferase. Engineered: yes. Peptide (phe)(arg)(tyr)(leu)(gly). Chain: c, d. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: aat. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: the peptide was chemically synthesized.

Resolution:

2.75Å R-factor: 0.207 R-free: 0.265

Authors:

K.Watanabe,Y.Toh,K.Tomita

Key ref:

K.Watanabe et al. (2007). Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase. Nature, 449, 867-871. PubMed id: 17891155 DOI: 10.1038/nature06167

Date:

04-Jun-07 Release date: 23-Oct-07

Protein chains

P0A8P1  (LFTR_ECOLI) -  Leucyl/phenylalanyl-tRNA--protein transferase from Escherichia coli (strain K12)

Seq: 234 a.a.

Struc: 229 a.a.

Enzyme reactions

• Enzyme class: E.C.2.3.2.6 - lysine/arginine leucyltransferase.
• Reaction:
  1. N-terminal L-lysyl-[protein] + L-leucyl-tRNA(Leu) = N-terminal L-leucyl-L-lysyl-[protein] + tRNA(Leu) + H(+)
  2. N-terminal L-arginyl-[protein] + L-leucyl-tRNA(Leu) = N-terminal L-leucyl-L-arginyl-[protein] + tRNA(Leu) + H(+)
• Cofactor: Monovalent cation

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nature06167

Nature 449:867-871 (2007)

PubMed id: 17891155

Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase.

K.Watanabe, Y.Toh, K.Suto, Y.Shimizu, N.Oka, T.Wada, K.Tomita.

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.

Selected figure(s)

Figure 3.
Figure 3: Superposition of two binary complex structures. a, Structural difference between the complex with rA-Phe (blue) and that with the product peptide (green). b, Detailed structural difference of the Gln 188 side chains between the two structures. c, Superposition of the two complexes. The complex with rA-Phe and that with the product peptide are coloured blue and dark green, respectively. The benzyl group of rA-Phe and the Arg in the product peptide are coloured cyan and green, respectively, and are shown in stick models.

Figure 4.
Figure 4: A model of the catalytic mechanism for peptide-bond formation by LF-transferase.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 449, 867-871) copyright 2007.

Figures were selected by the author.