4JC0

Crystal structure of Thermotoga maritima holo RimO in complex with pentasulfide, Northeast Structural Genomics Consortium Target VR77

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	TRAM	e4jc0A3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: TRAM	ECOD (1.6)
A	Radical_SAM	e4jc0A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Radical_SAM	ECOD (1.6)
A	UPF0004	e4jc0A4	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: UPF0004	ECOD (1.6)
B	TRAM	e4jc0B3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: TRAM	ECOD (1.6)
B	Radical_SAM	e4jc0B1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Radical_SAM	ECOD (1.6)
B	UPF0004	e4jc0B4	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: UPF0004	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.12160	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylthiotransferase, N-terminal domain	CATH (4.3.0)
A	3.30.750.210	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA		CATH (4.3.0)
A	3.30.750.200	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA		CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	3.40.50.12160	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylthiotransferase, N-terminal domain	CATH (4.3.0)
B	3.30.750.210	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA		CATH (4.3.0)
B	3.30.750.200	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA		CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF18693	TRAM domain (TRAM_2)	TRAM domain	This is a C-terminal TRAM (after TRM2, a family of uridine methylases, and MiaB) domain found in the methylthiotransferases RimO enzymes that catalyze the conversion of aspartate to 2-methylthio-aspartate (msD) in the S12 protein near the decoding ce ...	This is a C-terminal TRAM (after TRM2, a family of uridine methylases, and MiaB) domain found in the methylthiotransferases RimO enzymes that catalyze the conversion of aspartate to 2-methylthio-aspartate (msD) in the S12 protein near the decoding center in prokaryotic ribosomes. The TRAM domain in RimO, contains five anti-parallel beta-strands and docks on the surface of the Radical-SAM domain at the distal edge of its open TIM-barrel from its conserved [4Fe-4S] cluster [1].	Domain
A, B	PF04055	Radical SAM superfamily (Radical_SAM)	Radical SAM superfamily	Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.	Domain
A, B	PF00919	Uncharacterized protein family UPF0004 (UPF0004)	Uncharacterized protein family UPF0004	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Ribosomal protein S12 methylthiotransferase RimO	methylthiotransferase activity alkylthioltransferase activity transferase activity, transferring sulphur-containing groups transferase activity aspartic acid methylthiotransferase activity catalytic activity protein methylthiotransferase activity catalytic activity, acting on a protein iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding methylthiotransferase activity alkylthioltransferase activity transferase activity, transferring sulphur-containing groups transferase activity aspartic acid methylthiotransferase activity catalytic activity protein methylthiotransferase activity catalytic activity, acting on a protein iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	cellular biosynthetic process RNA metabolic process ncRNA processing nucleobase-containing compound metabolic process organic substance metabolic process heterocycle metabolic process tRNA processing organic substance biosynthetic process nitrogen compound metabolic process RNA processing cellular metabolic process tRNA modification cellular nitrogen compound metabolic process primary metabolic process cellular biosynthetic process RNA metabolic process ncRNA processing nucleobase-containing compound metabolic process organic substance metabolic process heterocycle metabolic process tRNA processing organic substance biosynthetic process nitrogen compound metabolic process RNA processing cellular metabolic process tRNA modification cellular nitrogen compound metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process RNA modification biosynthetic process ncRNA metabolic process macromolecule modification nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process cellular aromatic compound metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR007197	Radical SAM	Domain
A, B	IPR002792	TRAM domain	Domain
A, B	IPR006638	Elp3/MiaA/NifB-like, radical SAM core domain	Domain
A, B	IPR013848	Methylthiotransferase, N-terminal	Domain
A, B	IPR020612	Methylthiotransferase, conserved site	Conserved Site
A, B	IPR038135	Methylthiotransferase, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR005839	Methylthiotransferase	Family
A, B	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B	IPR023404	Radical SAM, alpha/beta horseshoe	Homologous Superfamily
A, B	IPR005840	Ribosomal protein uS12 methylthiotransferase RimO	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.