2Z3L

complex structure of LF-transferase and peptide A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

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

(2007) Nature 449: 867-871

  • DOI: 10.1038/nature06167
  • Primary Citation of Related Structures:  

  • 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. Howe ...

    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.


    Organizational Affiliation

    Institute of Biological Resources and Functions, National Institute of Advanced Industrial Sciences and Technology, 1-1-1, Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Leucyl/phenylalanyl-tRNA-protein transferase
A, B
233Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: aat (ycaA)
EC: 2.3.2.6
Find proteins for P0A8P1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8P1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide (PHE)(ARG)(TYR)(LEU)(GLY)
C, D
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAR
Query on TAR

Download SDF File 
Download CCD File 
A, B
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 115.540α = 90.00
b = 129.998β = 90.00
c = 38.436γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance