2Z3O | pdb_00002z3o

complex structure of LF-transferase and phenylalanine

• PDB DOI: https://doi.org/10.2210/pdb2Z3O/pdb

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


• Deposited: 2007-06-04 Released: 2007-10-23 
• Deposition Author(s): Watanabe, K., Toh, Y., Tomita, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.269 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

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

• PubMed: 17891155 
• DOI: https://doi.org/10.1038/nature06167
• Primary Citation 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. 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 53.67 kDa 
• Atom Count: 3,762 
• Modeled Residue Count: 463 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucyl/phenylalanyl-tRNA-protein transferase	A, B	233	Escherichia coli	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PHE	C [auth A], E [auth B]	PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-QMMMGPOBSA-N
TAR	D [auth A], F [auth B]	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.269 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.49	α = 90
b = 129.249	β = 90
c = 38.678	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-23 
Deposition Author(s): Watanabe, K., Toh, Y., Tomita, K.

Revision History  

• Version 1.0: 2007-10-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description