3EPJ

Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism

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	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8093072	3001077	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Simibi-like P-loop NTPases	8093070	3002018	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8093072	3001077	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Simibi-like P-loop NTPases	8093070	3002018	SCOP2B (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	IPPT	e3epjA2	A: alpha arrays	X: tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain (From Topology)	H: tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain (From Topology)	T: tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain	F: IPPT	ECOD (1.6)
A	IPT	e3epjA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: IPT	ECOD (1.6)
C [auth B]	IPPT	e3epjB2	A: alpha arrays	X: tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain (From Topology)	H: tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain (From Topology)	T: tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain	F: IPPT	ECOD (1.6)
C [auth B]	IPT	e3epjB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: IPT	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.10.20.140	Mainly Alpha	Orthogonal Bundle	Histone, subunit A		CATH (4.3.0)
A	3.30.160.60	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Classic Zinc Finger	CATH (4.3.0)
C [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C [auth B]	1.10.20.140	Mainly Alpha	Orthogonal Bundle	Histone, subunit A		CATH (4.3.0)
C [auth B]	3.30.160.60	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Classic Zinc Finger	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF01715	IPP transferase (IPPT)	IPP transferase	This is a family of IPP transferases EC:2.5.1.8 also known as tRNA delta(2)-isopentenylpyrophosphate transferase. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37) [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	tRNA isopentenyltransferase	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 catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity tRNA dimethylallyltransferase activity RNA binding tRNA binding nucleic acid binding cation binding metal ion binding	tRNA modification 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 RNA modification biosynthetic process tRNA processing macromolecule modification tRNA modification 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 RNA modification biosynthetic process tRNA processing macromolecule modification metabolic process cellular process macromolecule metabolic process RNA processing	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen cytosol
B [auth E], D [auth F]	tRNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR039657	Dimethylallyltransferase	Family
A, C [auth B]	IPR018022	IPP transferase	Family
A, C [auth B]	IPR030666	tRNA isopentenyltransferase, eukaryotes	Family
A, C [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.