2ZM5 | pdb_00002zm5

Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe)

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)
B	SCOP2B Superfamily	Simibi-like P-loop NTPases	8093069	3002018	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Simibi-like P-loop NTPases	8093069	3002018	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Simibi-like P-loop NTPases	8093069	3002018	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Simibi-like P-loop NTPases	8093069	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)
B		e2zm5B1	A: Long alpha-hairpin	X: C-terminal UvrC-binding domain of UvrB	H: C-terminal UvrC-binding domain of UvrB	T: Sulfotransfer_3	F:	ECOD (20:10:01)
B		e2zm5B2	A: Rubredoxin-like	X: Rubredoxin-related	H: Rubredoxin-related	T: VipB_2	F:	ECOD (20:10:01)
A		e2zm5A1	A: Anticodon-binding domain of Class II aaRS	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: HGTP_anticodon	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	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	1.10.20.140	Mainly Alpha	Orthogonal Bundle	Histone, subunit A		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, 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
C, D	tRNA(Phe)	-	-	-
A, B	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 cellular response to stimulus regulation of cellular process response to stimulus protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of translation in response to stress cellular response to stress response to stress protein metabolic process regulation of biosynthetic process regulation of biological process regulation of cytoplasmic translation in response to stress regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process translation regulation of gene expression regulation of translation cytoplasmic translation regulation of macromolecule biosynthetic process regulation of cytoplasmic translation regulation of metabolic process cellular response to heat response to heat response to abiotic stimulus response to temperature stimulus	-

InterPro: Protein Family Classification InterPro Database Homepage

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