9QW7 | pdb_00009qw7

The crystal structure of the adenyly transferase domain of Candida glabrata tRNA ligase

PDB DOI: https://doi.org/10.2210/pdb9QW7/pdb

Classification: LIGASE
Organism(s): Nakaseomyces glabratus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-04-14 Released: 2025-09-17
Deposition Author(s): McEwen, A.G., Poussin-Courmontagne, P., Giovinazzo, A., Tocchini-Valentini, G.D., Tocchini-Valentini, G.P., Pellegrini, M., Merolle, M.
Funding Organization(s): Instruct-ERIC Center (Strasbourg Centre), Agence Nationale de la Recherche (ANR), Ministero dell Universita e della Ricerca, European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.263 (Depositor), 0.263 (DCC)
R-Value Work:
0.218 (Depositor), 0.218 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The adaptability of the fungal tRNA ligase's ATP-binding pocket: a potential target for new antifungal drugs.

McEwen, A.G., Giovinazzo, A., Poussin-Courmontagne, P., Merolle, M., Tocchini-Valentini, G.P., Pellegrini, M., Tocchini-Valentini, G.D.

(2025) NAR Mol Med 2: ugaf028-ugaf028

PubMed: 41306651 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1093/narmme/ugaf028
Primary Citation of Related Structures:
9QW7

PubMed Abstract:
The transfer RNA (tRNA) ligase (TRL1) is a highly conserved multidomain protein that is the archetype of the recently characterized Rnl6 clade. This clade distinguishes itself through a distinct C-terminal domain that sets it apart from other RNA ligase families. TRL1 is an essential component of pre-tRNA splicing and the processing of the Ire1p (Inositol-requiring enzyme 1)-dependent noncanonical splicing of the messenger RNA (mRNA) coding for HAC-1 (Homologous to Activating Transcription Factor / cAMP Response Element-Binding Protein 1 (ATF/CREB1), a transcription factor critical for the unfolded protein response (UPR) in the kingdom of fungi. Here, we report the crystal structure of the N-terminal adenylyl transferase domain (LIG) from Candida glabrata (Nakaseomyces glabratus) . The asymmetric unit contained two molecules in complex with noncovalently linked adenosine monophosphate (AMP), revealing conformational differences. In comparison to previous studies, we observe two distinct and partially overlapping ligand-binding pockets, implying new specific residues involved in ligand binding and recognition. These insights on TRL1's ligand adaptability have important implications for the development of targeted therapies.

Organizational Affiliation

Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Centre National de la Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, Illkirch 67404, France.

Macromolecule Content

Total Structure Weight: 90.03 kDa
Atom Count: 6,146
Modeled Residue Count: 745
Deposited Residue Count: 768
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA ligase	A, B	384	Nakaseomyces glabratus	Mutation(s): 0 Gene Names: CAGL0M03091g EC: 6.5.1.3
UniProt
Find proteins for Q6FJW3 (Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138)) Explore Q6FJW3 Go to UniProtKB: Q6FJW3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6FJW3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.263 (Depositor), 0.263 (DCC)
R-Value Work: 0.218 (Depositor), 0.218 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.796	α = 90
b = 81.796	β = 90
c = 286.593	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-17

Deposition Author(s):

McEwen, A.G.

Poussin-Courmontagne, P.

Giovinazzo, A.

Tocchini-Valentini, G.D.

Tocchini-Valentini, G.P.

Pellegrini, M.

Merolle, M.

Funding Organization	Location	Grant Number
Instruct-ERIC Center (Strasbourg Centre)	France	PID 222
Agence Nationale de la Recherche (ANR)	France	ANR-10-INBS-000
Ministero dell Universita e della Ricerca	Italy	PRIN Cofin
Ministero dell Universita e della Ricerca	Italy	DSB AD009
European Union (EU)	European Union	EURASNET
European Union (EU)	European Union	EMMA-Infrafrontier
European Union (EU)	European Union	EUMODIC