3EXA | pdb_00003exa

Crystal structure of the full-length tRNA isopentenylpyrophosphate transferase (BH2366) from Bacillus halodurans, Northeast Structural Genomics Consortium target BhR41.

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)
D	d3exad1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Adenosine phosphateisopentenyltransferase (IPT)-like	Adenosine phosphateisopentenyltransferase (IPT)	(Halalkalibacterium halodurans ) [TaxId: 86665 ],	SCOPe (2.08)
D	d3exad2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Halalkalibacterium halodurans ) [TaxId: 86665 ],	SCOPe (2.08)
C	d3exac1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Adenosine phosphateisopentenyltransferase (IPT)-like	Adenosine phosphateisopentenyltransferase (IPT)	(Halalkalibacterium halodurans ) [TaxId: 86665 ],	SCOPe (2.08)
C	d3exac2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Halalkalibacterium halodurans ) [TaxId: 86665 ],	SCOPe (2.08)
B	d3exab1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Adenosine phosphateisopentenyltransferase (IPT)-like	Adenosine phosphateisopentenyltransferase (IPT)	(Halalkalibacterium halodurans ) [TaxId: 86665 ],	SCOPe (2.08)
B	d3exab2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Halalkalibacterium halodurans ) [TaxId: 86665 ],	SCOPe (2.08)
A	d3exaa1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Adenosine phosphateisopentenyltransferase (IPT)-like	Adenosine phosphateisopentenyltransferase (IPT)	(Halalkalibacterium halodurans ) [TaxId: 86665 ],	SCOPe (2.08)
A	d3exaa2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Halalkalibacterium halodurans ) [TaxId: 86665 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Simibi-like P-loop NTPases	8093065	3002018	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Simibi-like P-loop NTPases	8093065	3002018	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Simibi-like P-loop NTPases	8093065	3002018	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Simibi-like P-loop NTPases	8093065	3002018	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Simibi-like P-loop NTPases	8093065	3002018	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Simibi-like P-loop NTPases	8093065	3002018	SCOP2B (2022-06-29)
A	SCOP2 Family	IPP transferase-like	8049399	4006480	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Simibi-like P-loop NTPases	8093065	3002018	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)
D	EXOSC1	e3exaD1	A: alpha bundles	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: EXOSC1	ECOD (develop294)
C	EXOSC1	e3exaC1	A: alpha bundles	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: EXOSC1	ECOD (develop294)
B	EXOSC1	e3exaB1	A: alpha bundles	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: EXOSC1	ECOD (develop294)
A		e3exaA1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F:	ECOD (develop294)
A	IPPT	e3exaA2	A: alpha bundles	X: OB-fold	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: IPPT	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	1.10.287.890	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	1.10.287.890	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.10.287.890	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.10.287.890	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, B, C, D	tRNA delta(2)-isopentenylpyrophosphate transferase	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	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR039657	Dimethylallyltransferase	Family
A, B, C, D	IPR018022	IPP transferase	Family
A, B, C, D	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.