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- PDB-7xjz: Cryo-EM strucrture of Oryza sativa plastid glycyl-tRNA synthetase... -

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Basic information

Entry
Database: PDB / ID: 7xjz
TitleCryo-EM strucrture of Oryza sativa plastid glycyl-tRNA synthetase in complex with tRNA (tRNA binding state)
Components
  • Glycine--tRNA ligase
  • tRNA(gly)
KeywordsLIGASE/RNA / GlyRS2 / Glycine-tRNA ligase / tRNA selection / GlyRS tRNA complex / chloroplasts / LIGASE / LIGASE-RNA complex
Function / homology
Function and homology information


arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / embryo development ending in seed dormancy / regulation of embryonic development / chloroplast / mitochondrion / ATP binding
Similarity search - Function
Glycine-tRNA ligase, beta subunit / Glycyl-tRNA synthetase beta subunit / Glycine-tRNA ligase, alpha subunit / Glycine-tRNA synthetase, heterodimeric / Glycyl-tRNA synthetase alpha subunit / Heterodimeric glycyl-transfer RNA synthetases family profile. / DALR anticodon binding / DALR anticodon binding domain / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
RNA / RNA (> 10) / glycine--tRNA ligase
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
Oryza sativa (Asian cultivated rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsYu, Z. / Wu, Z. / Li, Y. / Lu, G. / Lin, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770784 China
National Natural Science Foundation of China (NSFC)31802147 China
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Structural basis of a two-step tRNA recognition mechanism for plastid glycyl-tRNA synthetase.
Authors: Zhaoli Yu / Zihan Wu / Ye Li / Qiang Hao / Xiaofeng Cao / Gregor M Blaha / Jinzhong Lin / Guoliang Lu /
Abstract: Two types of glycyl-tRNA synthetase (GlyRS) are known, the α2 and the α2β2 GlyRSs. Both types of synthetase employ a class II catalytic domain to aminoacylate tRNAGly. In plastids and some ...Two types of glycyl-tRNA synthetase (GlyRS) are known, the α2 and the α2β2 GlyRSs. Both types of synthetase employ a class II catalytic domain to aminoacylate tRNAGly. In plastids and some bacteria, the α and β subunits are fused and are designated as (αβ)2 GlyRSs. While the tRNA recognition and aminoacylation mechanisms are well understood for α2 GlyRSs, little is known about the mechanisms for α2β2/(αβ)2 GlyRSs. Here we describe structures of the (αβ)2 GlyRS from Oryza sativa chloroplast by itself and in complex with cognate tRNAGly. The set of structures reveals that the U-shaped β half of the synthetase selects the tRNA in a two-step manner. In the first step, the synthetase engages the elbow and the anticodon base C35 of the tRNA. In the second step, the tRNA has rotated ∼9° toward the catalytic centre. The synthetase probes the tRNA for the presence of anticodon base C36 and discriminator base C73. This intricate mechanism enables the tRNA to access the active site of the synthetase from a direction opposite to that of most other class II synthetases.
History
DepositionApr 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycine--tRNA ligase
B: tRNA(gly)


Theoretical massNumber of molelcules
Total (without water)140,9572
Polymers140,9572
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Glycine--tRNA ligase


Mass: 117050.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Os06g0103600, OsJ_19814, OSNPB_060103600 / Plasmid: pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: Q0DFB6, glycine-tRNA ligase
#2: RNA chain tRNA(gly)


Mass: 23906.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1complexCOMPLEXall0RECOMBINANT
2glycyl-tRNA synthetaseCOMPLEX#11RECOMBINANT
3tRNACOMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Oryza sativa subsp. japonica (Japanese rice)39947
23Oryza sativa (Asian cultivated rice)4530
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli BL21(DE3) (bacteria)469008
23in vitro transcription vector pT7-TP(deltai) (others)905931
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179986 / Symmetry type: POINT
RefinementCross valid method: NONE
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01329614
ELECTRON MICROSCOPYf_angle_d1.309413389
ELECTRON MICROSCOPYf_chiral_restr0.04491577
ELECTRON MICROSCOPYf_plane_restr0.00751461
ELECTRON MICROSCOPYf_dihedral_angle_d9.99011931

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