5ONH

Quaternary complex of wild type E. coli leucyl-tRNA synthetase with tRNA(leu), leucyl-adenylate analogue, and post-transfer editing analogue of norvaline in the aminoacylation conformation

PDB DOI: https://doi.org/10.2210/pdb5ONH/pdb
NDB: 5ONH

Classification: LIGASE
Organism(s): Escherichia coli K-12, Escherichia coli
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2017-08-03 Released: 2017-11-15
Deposition Author(s): Palencia, A., Cusack, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.257
R-Value Work: 0.223
R-Value Observed: 0.224

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase.

Dulic, M., Cvetesic, N., Zivkovic, I., Palencia, A., Cusack, S., Bertosa, B., Gruic-Sovulj, I.

(2018) J Mol Biol 430: 1-16

PubMed: 29111343 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2017.10.024
Primary Citation of Related Structures:
5OMW, 5ON2, 5ON3, 5ONH

PubMed Abstract:

The intrinsic editing capacities of aminoacyl-tRNA synthetases ensure a high-fidelity translation of the amino acids that possess effective non-cognate aminoacylation surrogates. The dominant error-correction pathway comprises deacylation of misaminoacylated tRNA within the aminoacyl-tRNA synthetase editing site. To assess the origin of specificity of Escherichia coli leucyl-tRNA synthetase (LeuRS) against the cognate aminoacylation product in editing, we followed binding and catalysis independently using cognate leucyl- and non-cognate norvalyl-tRNA ^Leu and their non-hydrolyzable analogues. We found that the amino acid part (leucine versus norvaline) of (mis)aminoacyl-tRNAs can contribute approximately 10-fold to ground-state discrimination at the editing site. In sharp contrast, the rate of deacylation of leucyl- and norvalyl-tRNA ^Leu differed by about 10 ⁴-fold. We further established the critical role for the A76 3'-OH group of the tRNA ^Leu in post-transfer editing, which supports the substrate-assisted deacylation mechanism. Interestingly, the abrogation of the LeuRS specificity determinant threonine 252 did not improve the affinity of the editing site for the cognate leucine as expected, but instead substantially enhanced the rate of leucyl-tRNA ^Leu hydrolysis. In line with that, molecular dynamics simulations revealed that the wild-type enzyme, but not the T252A mutant, enforced leucine to adopt the side-chain conformation that promotes the steric exclusion of a putative catalytic water. Our data demonstrated that the LeuRS editing site exhibits amino acid specificity of kinetic origin, arguing against the anticipated prominent role of steric exclusion in the rejection of leucine. This feature distinguishes editing from the synthetic site, which relies on ground-state discrimination in amino acid selection.

Organizational Affiliation:

Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia. Electronic address: gruic@chem.pmf.hr.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine--tRNA ligase	A, C [auth D]	880	Escherichia coli K-12	Mutation(s): 0 Gene Names: leuS, b0642, JW0637 EC: 6.1.1.4
UniProt
Find proteins for P07813 (Escherichia coli (strain K12)) Explore P07813 Go to UniProtKB: P07813
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07813
Protein Feature View Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
L-leucyl-tRNA(Leu)	B, D [auth E]	87	Escherichia coli
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LSS Query on LSS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth D]	F [auth A], J [auth D]	5'-O-(L-leucylsulfamoyl)adenosine C₁₆ H₂₅ N₇ O₇ S XFEDFDTWJLGMBO-LEJQEAHTSA-N		Ligand Interaction
VRT Query on VRT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth D]	G [auth A], K [auth D]	2'-(L-NORVALYL)AMINO-2'-DEOXYADENOSINE C₁₅ H₂₃ N₇ O₄ NWKNSTYARDJRIZ-IEUWZBGXSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain E [auth A] MOL2 format, chain I [auth D] MOL2 format, chain E [auth A]	E [auth A], I [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain H [auth B] MOL2 format, chain L [auth E] MOL2 format, chain H [auth B]	H [auth B], L [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction