Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58.89 kDa 
• Atom Count: 3814 
• Residue Count: 464 
• Unique protein chains: 1

2DPT

Leucyl/phenylalanyl-tRNA-protein transferase complexed with puromycin

• DOI: 10.2210/pdb2DPT/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-05-14 Released: 2007-01-02 
• Deposition Author(s): Suto, K., Shimizu, Y., Tomita, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.263 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 

Literature

Crystal structures of leucyl/phenylalanyl-tRNA-protein transferase and its complex with an aminoacyl-tRNA analog

Suto, K., Shimizu, Y., Watanabe, K., Ueda, T., Fukai, S., Nureki, O., Tomita, K.

(2006) EMBO J 25: 5942-5950

• PubMed: 17110926 
• DOI: 10.1038/sj.emboj.7601433
• Primary Citation of Related Structures:  
  2DPT, 2DPS


• PubMed Abstract: 
  

Eubacterial leucyl/phenylalanyl-tRNA protein transferase (L/F-transferase), encoded by the aat gene, conjugates leucine or phenylalanine to the N-terminal Arg or Lys residue of proteins, using Leu-tRNA(Leu) or Phe-tRNA(Phe) as a substrate. The resulting N-terminal Leu or Phe acts as a degradation signal for the ClpS-ClpAP-mediated N-end rule protein degradation pathway. Here, we present the crystal structures of Escherichia coli L/F-transferase and its complex with an aminoacyl-tRNA analog, puromycin. The C-terminal domain of L/F-transferase consists of the GCN5-related N-acetyltransferase fold, commonly observed in the acetyltransferase superfamily. The p-methoxybenzyl group of puromycin, corresponding to the side chain of Leu or Phe of Leu-tRNA(Leu) or Phe-tRNA(Phe), is accommodated in a highly hydrophobic pocket, with a shape and size suitable for hydrophobic amino-acid residues lacking a branched beta-carbon, such as leucine and phenylalanine. Structure-based mutagenesis of L/F-transferase revealed its substrate specificity. Furthermore, we present a model of the L/F-transferase complex with tRNA and substrate proteins bearing an N-terminal Arg or Lys.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucyl/phenylalanyl-tRNA--protein transferase	A, B	254	Escherichia coli	Mutation(s): 0  EC: 2.3.2.6
Find proteins for P0A8P1 (Escherichia coli (strain K12)) Explore P0A8P1  Go to UniProtKB:  P0A8P1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PUY	A, B	PUROMYCIN C22 H29 N7 O5 RXWNCPJZOCPEPQ-NVWDDTSBSA-N
TAR	A, B	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.263 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.662	α = 90
b = 129.139	β = 90
c = 38.571	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-14 
• Released Date: 2007-01-02 
Deposition Author(s): Suto, K., Shimizu, Y., Tomita, K.

Revision History 

• Version 1.0: 2007-01-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance