4JC0 | pdb_00004jc0

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	Sas-5-like_implico	e4jc0A1	A: alpha bundles	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: Sas-5-like_implico	ECOD (develop294)
A	Peripla_BP_2	e4jc0A4	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Peripla_BP_2	ECOD (develop294)
B	Sas-5-like_implico	e4jc0B1	A: alpha bundles	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: Sas-5-like_implico	ECOD (develop294)
B	LRR_1,LRR_8	e4jc0B4	A: alpha bundles	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: LRR_1,LRR_8	ECOD (develop294)

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	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 anatomical structure intracellular anatomical structure cytoplasm 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	IPR058240	Radical SAM superfamily	Homologous Superfamily
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 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.