2Z3K

complex structure of LF-transferase and rAF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    2Z3K, 2Z3L, 2Z3M, 2Z3N, 2Z3O, 2Z3P

  • 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Leucyl/phenylalanyl-tRNA-protein transferaseA, B233Escherichia coliMutation(s): 0 
Gene Names: aat
EC: 2.3.2.6
UniProt
Find proteins for P0A8P1 (Escherichia coli (strain K12))
Explore P0A8P1 
Go to UniProtKB:  P0A8P1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XYA (Subject of Investigation/LOI)
Query on XYA

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]2-(6-AMINO-OCTAHYDRO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL
C10 H13 N5 O4
OIRDTQYFTABQOQ-GAWUUDPSSA-N
 Ligand Interaction
PHE (Subject of Investigation/LOI)
Query on PHE

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
TAR
Query on TAR

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.106α = 90
b = 129.846β = 90
c = 38.691γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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