PDBsum entry 2dps

Transferase

PDB id: 2dps

Contents

Protein chains

228 a.a. *

Waters ×70

* Residue conservation analysis

PDB id:

2dps

Name:

Transferase

Title:

Structure of leucyl/phenylalanyl-tRNA-protein transferase

Structure:

Leucyl/phenylalanyl-tRNA--protein transferase. Chain: a, b. Synonym: l/f-transferase, leucyltransferase, phenyalanyltransferase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.40Å R-factor: 0.220 R-free: 0.272

Authors:

K.Suto,Y.Shimizu,K.Tomita

Key ref:

K.Suto et al. (2006). Crystal structures of leucyl/phenylalanyl-tRNA-protein transferase and its complex with an aminoacyl-tRNA analog. EMBO J, 25, 5942-5950. PubMed id: 17110926 DOI: 10.1038/sj.emboj.7601433

Date:

14-May-06 Release date: 02-Jan-07

Protein chains

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

Seq: 234 a.a.

Struc: 228 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/sj.emboj.7601433

EMBO J 25:5942-5950 (2006)

PubMed id: 17110926

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

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

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.

Selected figure(s)

Figure 1.
Figure 1 Overall architecture of E. coli L/F-transferase. (A) Stereo view of the E. coli L/F-transferase structure. The NH[2]-terminal domain (residues 2–62) and the COOH-terminal domain (residues 63–232) are colored blue and green, respectively. The puromycin bound to the hydrophobic pocket is colored yellow. (B) Topology diagram of L/F-transferase. The rimmed elements in the COOH-terminal domain ( 3– 5) and ( 5– 12) are common to the GNAT superfamily fold. The -helices and -strands in the COOH-terminal domains are colored red and yellow, respectively. (C) Comparison of the structures of E. coli L/F-transferase (left), W. viridescens FemX (wvFemX; middle, PDB accession number 1P4N; Biarrotte-Sorin et al, 2004) and S. aureus FemA (saFemA; PDB accession number 1LRZ; Benson et al, 2002). The COOH-terminal domain of L/F-transferase is topologically similar to the domain 2's of wvFemX and saFemA. The conserved -helices and -strands in L/F-transferase, wvFemX and saFemA, are colored red and yellow, respectively.

Figure 3.
Figure 3 Recognition of the puromycin by E. coli L/F-transferase. (A) Chemical structure of puromycin (left) and that of the 3'-ends of Leu-tRNA^Leu and Phe-tRNA^Phe (middle and right, respectively). The amino-acid moiety and the base moiety are colored pink and blue, respectively. (B) |Fo-Fc| omit map of puromycin (contour level 3.0 ). (C) Recognition of the p-methoxybenzyl group and the puromycin base by the hydrophobic pocket, as shown by a surface model. (D) Ribbon model of (C). The hydrophobic amino acid involved in the recognition of the p-methoxybenzyl group and the base moiety of puromycin are colored green and blue, respectively. (E) The C-shaped edge of the hydrophobic pocket is composed of continuous amino-acid residues (Gly155-Glu156-Ser157-Met158; colored yellow and highlighted). The -, - and -carbons of puromycin are also shown.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 5942-5950) copyright 2006.

Figures were selected by the author.