2HSN | pdb_00002hsn

Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2hsnb_	All alpha proteins	GST C-terminal domain-like	GST C-terminal domain-like	Arc1p N-terminal domain-like	GU4 nucleic-binding protein 1, Arc1p	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	GST C-terminal domain-like	8034258	3000305	SCOP2B (2022-06-29)
A	SCOP2 Family	Cytoplasmic MetRS N-terminal domain-like	8045281	4004390	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GST C-terminal domain-like	8089968	3000305	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Thioredoxin-like	8089967	3000031	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	GST_C_Arc1p_N_like	e2hsnB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Glutathione S-transferase (GST)-C (From Topology)	T: Glutathione S-transferase (GST)-C	F: GST_C_Arc1p_N_like	ECOD (1.6)
A	MetRS-N_C	e2hsnA2	A: alpha superhelices	X: Repetitive alpha hairpins	H: Glutathione S-transferase (GST)-C (From Topology)	T: Glutathione S-transferase (GST)-C	F: MetRS-N_C	ECOD (1.6)
A	MetRS-N_N	e2hsnA1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: MetRS-N_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.20.1050.10	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)
A	3.40.30.170	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin		CATH (4.3.0)
A	1.20.1050.110	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF21972	Nuclear-export cofactor Arc1p (Arc1p_N_like)	Nuclear-export cofactor Arc1p	This is the N-terminal domain of nuclear-export cofactor Arc1p (Arc1p-N). Arc1p-N and GluRS-N are known to be necessary and sufficient for formation of the yeast aaRS complex in vivo and in vitro. They are likely to form a stable complex with each ot ...	This is the N-terminal domain of nuclear-export cofactor Arc1p (Arc1p-N). Arc1p-N and GluRS-N are known to be necessary and sufficient for formation of the yeast aaRS complex in vivo and in vitro. They are likely to form a stable complex with each other. Arc1p-N adopts a fold similar to the C-terminal domain of glutathione S-transferase (GST-C).	Domain
A	PF09635	MetRS-N binding domain (MetRS-N)	MetRS-N binding domain	The MetRS-N domain binds an Arc1-P domain in a tetrameric complex resembling a classical GST homo-dimer. Domain-swapping between symmetrically related MetRS-N and Arc1p-N domains generates a 2:2 tetramer held together by van der Waals forces. This do ...	The MetRS-N domain binds an Arc1-P domain in a tetrameric complex resembling a classical GST homo-dimer. Domain-swapping between symmetrically related MetRS-N and Arc1p-N domains generates a 2:2 tetramer held together by van der Waals forces. This domain is necessary for formation of the aminoacyl-tRNA synthetase complex necessary for tRNA nuclear export and shuttling as part of the translational apparatus. The domain is associated with Pfam:PF09334.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	GU4 nucleic-binding protein 1	phosphatidylinositol-3,5-bisphosphate binding binding ion binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding small molecule binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity phosphatidylinositol-3,5-bisphosphate binding binding ion binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding small molecule binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity phosphatidylinositol-3-phosphate binding RNA binding tRNA binding nucleic acid binding	amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process glutamyl-tRNA aminoacylation methionyl-tRNA aminoacylation	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule protein-containing complex methionyl glutamyl tRNA synthetase complex
A	Methionyl-tRNA synthetase, cytoplasmic	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity methionine-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity RNA binding sequence-specific mRNA binding nucleic acid binding mRNA binding	amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process glutamyl-tRNA aminoacylation methionyl-tRNA aminoacylation	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule protein-containing complex catalytic complex aminoacyl-tRNA synthetase multienzyme complex intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule protein-containing complex catalytic complex aminoacyl-tRNA synthetase multienzyme complex intracellular protein-containing complex cytosol methionyl glutamyl tRNA synthetase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR002547	tRNA-binding domain	Domain
B	IPR053836	Nuclear-export cofactor Arc1-like, N-terminal domain	Domain
B	IPR051270	Tyrosine-tRNA ligase and regulatory protein	Family
B	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
B	IPR036282	Glutathione S-transferase, C-terminal domain superfamily	Homologous Superfamily
A	IPR023458	Methionine-tRNA ligase, type 1	Family
A	IPR041872	Methionyl-tRNA synthetase, anticodon-binding domain	Domain
A	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
A	IPR015413	Methionyl/Leucyl tRNA synthetase	Domain
A	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A	IPR014758	Methionyl-tRNA synthetase	Family
A	IPR009080	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Homologous Superfamily
A	IPR033911	Methioninyl-tRNA synthetase core domain	Domain
A	IPR029038	Methionyl-tRNA synthetase, Zn-domain	Homologous Superfamily
A	IPR018285	Methionyl-tRNA synthetase, N-terminal heteromerisation domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.