PDBsum entry 1obc

Synthetase

PDB id: 1obc

Contents

Protein chain

811 a.a. *

Ligands

LEU

NVA-2AD

LMS

Metals

_ZN ×2

Waters ×487

* Residue conservation analysis

PDB id:

1obc

Name:

Synthetase

Title:

Leucyl-tRNA synthetase from thermus thermophilus complexed with a post-transfer editing substrate analogue

Structure:

Leucyl-tRNA synthetase. Chain: a. Engineered: yes. Other_details: enzyme contains 878 residues and two zinc atoms

Source:

Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.10Å R-factor: 0.193 R-free: 0.225

Authors:

S.Cusack,A.Yaremchuk,M.Tukalo

Key ref:

T.L.Lincecum et al. (2003). Structural and mechanistic basis of pre- and posttransfer editing by leucyl-tRNA synthetase. Mol Cell, 11, 951-963. PubMed id: 12718881 DOI: 10.1016/S1097-2765(03)00098-4

Date:

30-Jan-03 Release date: 09-May-03

Protein chain

Q72GM3  (Q72GM3_THET2) -  Leucine--tRNA ligase from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 878 a.a.

Struc: 811 a.a.

Enzyme reactions

• Enzyme class: E.C.6.1.1.4 - leucine--tRNA ligase.
• Reaction: tRNA(Leu) + L-leucine + ATP = L-leucyl-tRNA(Leu) + AMP + diphosphate

tRNA(Leu) + L-leucine (Bound ligand (Het Group name = LEU) matches with 88.89% similarity) + ATP = L-leucyl-tRNA(Leu) (Bound ligand (Het Group name = LMS) matches with 70.37% similarity) + AMP + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/S1097-2765(03)00098-4

Mol Cell 11:951-963 (2003)

PubMed id: 12718881

Structural and mechanistic basis of pre- and posttransfer editing by leucyl-tRNA synthetase.

T.L.Lincecum, M.Tukalo, A.Yaremchuk, R.S.Mursinna, A.M.Williams, B.S.Sproat, W.Van Den Eynde, A.Link, S.Van Calenbergh, M.Grøtli, S.A.Martinis, S.Cusack.

ABSTRACT

The aminoacyl-tRNA synthetases link tRNAs with their cognate amino acid. In some cases, their fidelity relies on hydrolytic editing that destroys incorrectly activated amino acids or mischarged tRNAs. We present structures of leucyl-tRNA synthetase complexed with analogs of the distinct pre- and posttransfer editing substrates. The editing active site binds the two different substrates using a single amino acid discriminatory pocket while preserving the same mode of adenine recognition. This suggests a similar mechanism of hydrolysis for both editing substrates that depends on a key, completely conserved aspartic acid, which interacts with the alpha-amino group of the noncognate amino acid and positions both substrates for hydrolysis. Our results demonstrate the economy by which a single active site accommodates two distinct substrates in a proofreading process critical to the fidelity of protein synthesis.

Selected figure(s)

Figure 1.
Figure 1. Editing Reactions, Editing Substrates, and Sequence Conservation in the Editing Domain(A) LeuRS aminoacylation and editing reactions. Editing reactions are indicated by the dashed arrows. Although tRNA has been shown to be a cofactor for pretransfer editing by IleRS (Baldwin and Berg, 1966), its role in LeuRS editing is unknown.(B) Diagrams of the analogs used in this work of LeuRS pre- and posttransfer editing substrates for the case of noncognate norvaline (Nva). Left: posttransfer substrate analog, 2′-(L-norvalyl)amino-2′-deoxyadenosine (Nva2AA), mimicking the 3′ end of the aminoacyl-2′-ester Nva-tRNA^Leu. Right: pretransfer substrate analog, 5′-O-[N-(L-norvalyl)sulphamoyl]adenosine (NvaAMS), a sulfamoyl analog of norvalyl-adenylate. In each case, the labile ester linkages were replaced by a nonhydrolyzable amino linkage to permit structural studies.(C) Alignment of conserved regions within the editing (CP1) domain of selected LeuRS (L), ValRS (V), and IleRS (I) enzymes. The “threonine-rich region” contains two highly conserved threonines (arrowed) discussed in the text. In the second region, separated by a bracket, a conserved glycine-rich loop is followed by a completely conserved aspartic acid (arrowed) that was mutated to alanine. Abbreviations: Sc, S. cerevisiae; Ce, Caenorhabditis elegans; Hs, Homo sapiens; Nc, Neurospora crassa; Ec, E. coli; Tt, Thermus thermophilus; Bs, Bacillus subtilis; Gs, Geobacillus stearothermophilus; Sa, Staphylococcus aureus; cyt, cytoplasmic; mit, mitochondrial.

Figure 2.
Figure 2. Electron Density of the Editing Substrates(A) Simulated omit map (Brunger et al., 1998) for the pretransfer substrate analog (NvaAMS) in the editing (top) and synthetic (bottom) active site. Resolution is 2.2 Å. In both molecules, the ribose is in the C2′ endo conformation.(B) Location of the NvaAMS in the synthetic and editing active sites of LeuRSTT.(C) Unbiased difference map (2.0 Å resolution) for the posttransfer editing substrate analog (Nva2AA) in the editing site. The ribose is in the C3′ endo conformation.(D) Competitive inhibition of E. coli LeuRS editing of Ile-tRNA^Leu by Nva2AA. Editing of Ile-tRNA^Leu by wild-type E. coli LeuRS in the absence of inhibitor exhibited a K[M] of 0.2 μM.

The above figures are reprinted by permission from Cell Press: Mol Cell (2003, 11, 951-963) copyright 2003.

Figures were selected by an automated process.