4E1B | pdb_00004e1b

Re-refinement of PDB entry 2EQA - SUA5 protein from Sulfolobus tokodaii with bound threonylcarbamoyladenylate

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	YrdC/Sua5-like	8004466	4000384	SCOP2 (2022-06-29)
A	SCOP2 Family	Sua5 C-terminal domain-like	8004467	4000386	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YrdC/RibB-like	8017697	3000166	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sua5 C-terminal domain-like	8019807	3002028	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)
A		e4e1bA1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: Defensin_2	F:	ECOD (20:10:01)
A		e4e1bA2	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T:	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.870.10	Alpha Beta	Alpha-Beta Complex	DHBP synthase	DHBP synthase	CATH (4.3.0)
A	3.40.50.11030	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Threonylcarbamoyl-AMP synthase, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03481	Threonylcarbamoyl-AMP synthase, C-terminal domain (Sua5_C)	Threonylcarbamoyl-AMP synthase, C-terminal domain	This domain can be found in the C terminus of threonylcarbamoyl-AMP synthases, including Sua5 from Saccharomyces cerevisiae and YwlC from Bacillus subtilis. Threonylcarbamoyl-AMP synthase is required for the formation of a threonylcarbamoyl group on ...	This domain can be found in the C terminus of threonylcarbamoyl-AMP synthases, including Sua5 from Saccharomyces cerevisiae and YwlC from Bacillus subtilis. Threonylcarbamoyl-AMP synthase is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t6A37) in tRNAs that read codons beginning with adenine [1,2]. This domain adopts the Rossmann fold and may be involved in GTP and/or tRNA binding based on structural similarity with both GTP and tRNA binding proteins [3].	Domain
A	PF01300	Telomere recombination (Sua5_yciO_yrdC)	Telomere recombination	This domain has been shown to bind preferentially to dsRNA [1]. The domain is found in SUA5 Swiss:P32579 as well as HypF and YrdC Swiss:P45748. It has also been shown to be required for telomere recombniation in yeast.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	YrdC/Sua5 family protein	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 L-threonylcarbamoyladenylate synthase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding double-stranded RNA binding nucleic acid binding tRNA binding	biological regulation regulation of biological quality regulation of translational fidelity RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process biological regulation regulation of biological quality regulation of translational fidelity RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process cellular process macromolecule metabolic process RNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR010923	tRNA threonylcarbamoyladenosine biosynthesis protein SUA5	Family
A	IPR005145	Threonylcarbamoyl-AMP synthase, C-terminal domain	Domain
A	IPR050156	Threonylcarbamoyl-AMP synthase, SUA5	Family
A	IPR017945	DHBP synthase RibB-like alpha/beta domain superfamily	Homologous Superfamily
A	IPR006070	Threonylcarbamoyl-AMP synthase-like domain	Domain
A	IPR038385	Threonylcarbamoyl-AMP synthase, C-terminal domain superfamily	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.