2ITB

CRYSTAL STRUCTURE OF A PUTATIVE TRNA-(MS(2)IO(6)A)-HYDROXYLASE (PP_2188) FROM PSEUDOMONAS PUTIDA KT2440 AT 2.05 A RESOLUTION

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)
A	d2itba1	All alpha proteins	Ferritin-like	Ferritin-like	MiaE-like	Putative tRNA-(Ms(2)io(6)a)-hydroxylase PP2188	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
B	d2itbb_	All alpha proteins	Ferritin-like	Ferritin-like	MiaE-like	Putative tRNA-(Ms(2)io(6)a)-hydroxylase PP2188	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	MiaE-like	8022201	4001288	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ferritin-like	8034581	3001658	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ferritin-like	8034581	3001658	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	PF06175	e2itbA1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: PF06175	ECOD (1.6)
B	PF06175	e2itbB1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: PF06175	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
B	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF06175	tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE) (MiaE)	tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)	This family consists of several bacterial tRNA-(MS(2)IO(6)A)-hydroxylase (MiaE) proteins. The modified nucleoside 2-methylthio-N-6-isopentenyl adenosine (ms2i6A) is present at position 37 (3' of the anticodon) of tRNAs that read codons beginning with ...	This family consists of several bacterial tRNA-(MS(2)IO(6)A)-hydroxylase (MiaE) proteins. The modified nucleoside 2-methylthio-N-6-isopentenyl adenosine (ms2i6A) is present at position 37 (3' of the anticodon) of tRNAs that read codons beginning with U except tRNA(I,V Ser) in Escherichia coli. Salmonella typhimurium 2-methylthio-cis-ribozeatin (ms2io6A) is found in tRNA, probably in the corresponding species that have ms2i6A in E. coli. The miaE gene is absent in E. coli, a finding consistent with the absence of the hydroxylated derivative of ms2i6A in this species [1-2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	TRNA-(Ms(2)io(6)a)-hydroxylase, putative	monooxygenase activity oxidoreductase activity catalytic activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity catalytic activity, acting on a tRNA cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR012347	Ferritin-like	Homologous Superfamily
A, B	IPR009078	Ferritin-like superfamily	Homologous Superfamily
A, B	IPR010386	tRNA-hydroxylase MiaE	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.