8WND | pdb_00008wnd

Crystal structure of Saccharomyces cerevisiae isoleucyl-tRNA synthetase in complex with tRNA(Ile) and isoleucine

PDB DOI: https://doi.org/10.2210/pdb8WND/pdb
NAKB: 8WND

Classification: LIGASE/RNA
Organism(s): Saccharomyces cerevisiae, Escherichia coli
Expression System: Escherichia coli 0.1197
Mutation(s): No

Deposited: 2023-10-05 Released: 2024-10-09
Deposition Author(s): Chen, B., Yi, F., Zhou, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.268 (Depositor), 0.270 (DCC)
R-Value Work:
0.230 (Depositor), 0.234 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The mechanism of discriminative aminoacylation by isoleucyl-tRNA synthetase based on wobble nucleotide recognition.

Chen, B., Yi, F., Luo, Z., Lu, F., Liu, H., Luo, S., Gu, Q., Zhou, H.

(2024) Nat Commun 15: 10817-10817

PubMed: 39738040 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-55183-0
Primary Citation of Related Structures:
8WND, 8Z1P

PubMed Abstract:
The faithful charging of amino acids to cognate tRNAs by aminoacyl-tRNA synthetases (AARSs) determines the fidelity of protein translation. Isoleucyl-tRNA synthetase (IleRS) distinguishes tRNA ^Ile from tRNA ^Met solely based on the nucleotide at wobble position (N34), and a single substitution at N34 could exchange the aminoacylation specificity between two tRNAs. Here, we report the structural and biochemical mechanism of N34 recognition-based tRNA discrimination by Saccharomyces cerevisiae IleRS (ScIleRS). ScIleRS utilizes a eukaryotic/archaeal-specific arginine as the H-bond donor to recognize the common carbonyl group (H-bond acceptor) of various N34s of tRNA ^Ile, which induces mutual structural adaptations between ScIleRS and tRNA ^Ile to achieve a preferable editing state. C34 of unmodified tRNA ^Ile(CAU) (behaves like tRNA ^Met) lacks a relevant H-bond acceptor, which disrupts key H-bonding interactions and structural adaptations and suspends the ScIleRS·tRNA ^Ile(CAU) complex in an initial non-reactive state. This wobble nucleotide recognition-based structural adaptation provides mechanistic insights into selective tRNA aminoacylation by AARSs.

Organizational Affiliation

State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.

Macromolecule Content

Total Structure Weight: 299.36 kDa
Atom Count: 18,444
Modeled Residue Count: 2,144
Deposited Residue Count: 2,314
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
isoleucine--tRNA ligase	A, C [auth B]	1,080	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ILS1 EC: 6.1.1.5
UniProt
Find proteins for P09436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P09436 Go to UniProtKB: P09436
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09436
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
tRNA(Ile)	B [auth T], D [auth R]	77	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ILE (Subject of Investigation/LOI) Query on ILE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B]	ISOLEUCINE C₆ H₁₃ N O₂ AGPKZVBTJJNPAG-WHFBIAKZSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]