3AWI | pdb_00003awi

Bifunctional tRNA modification enzyme MnmC from Escherichia coli

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)
F	SCOP2B Superfamily	Flavoreductase-like	8090685	3000055	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090683	3000118	SCOP2B (2022-06-29)
E	SCOP2 Family	MnmC, N-terminal methyltransferase domain	8047189	4005497	SCOP2 (2022-06-29)
E	SCOP2 Family	D-aminoacid oxidase-like	8090684	4000124	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090683	3000118	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Flavoreductase-like	8090685	3000055	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090683	3000118	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Flavoreductase-like	8090685	3000055	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090683	3000118	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Flavoreductase-like	8090685	3000055	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090683	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Flavoreductase-like	8090685	3000055	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Flavoreductase-like	8090685	3000055	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090683	3000118	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)
F	Methyltr_RsmB-F	e3awiF5	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: Methyltr_RsmB-F	ECOD (v294.1)
F	Spectrin	e3awiF2	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: Spectrin	ECOD (v294.1)
E	Methyltr_RsmB-F	e3awiE5	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: Methyltr_RsmB-F	ECOD (v294.1)
E	Spectrin	e3awiE2	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: Spectrin	ECOD (v294.1)
D	DcpS_C	e3awiD11	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: DcpS_C	ECOD (v294.1)
D	Spectrin	e3awiD2	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: Spectrin	ECOD (v294.1)
C	Methyltr_RsmB-F	e3awiC5	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: Methyltr_RsmB-F	ECOD (v294.1)
C	MMS1_N	e3awiC1	A: a/b three-layered sandwiches	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (v294.1)
B	Methyltr_RsmB-F	e3awiB5	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: Methyltr_RsmB-F	ECOD (v294.1)
B	Spectrin	e3awiB2	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: Spectrin	ECOD (v294.1)
A	Methyltr_RsmB-F	e3awiA7	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: Methyltr_RsmB-F	ECOD (v294.1)
A	MMS1_N	e3awiA1	A: a/b three-layered sandwiches	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
F	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
F	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (4.3.0)
E	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
E	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
E	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (4.3.0)
D	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
D	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
D	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (4.3.0)
C	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
C	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
C	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (4.3.0)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
B	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF05430	S-adenosyl-L-methionine-dependent methyltransferase (Methyltransf_30)	S-adenosyl-L-methionine-dependent methyltransferase	-	Family
A, B, C, D, E A, B, C, D, E, F	PF01266	FAD dependent oxidoreductase (DAO)	FAD dependent oxidoreductase	This family includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase EC:1.1.99.5, Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC	tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups tRNA (uridine) methyltransferase activity catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity tRNA (5-methylaminomethyl-2-thiouridylate)(34)-methyltransferase activity methyltransferase activity catalytic activity FAD binding flavin adenine dinucleotide binding tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups tRNA (uridine) methyltransferase activity catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity tRNA (5-methylaminomethyl-2-thiouridylate)(34)-methyltransferase activity methyltransferase activity catalytic activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors	RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA modification biosynthetic process methylation macromolecule modification metabolic process cellular process macromolecule metabolic process RNA methylation tRNA methylation tRNA wobble uridine modification tRNA wobble base modification	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR008471	MnmC-like methyltransferase	Domain
A, B, C, D, E A, B, C, D, E, F	IPR023032	tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC	Family
A, B, C, D, E A, B, C, D, E, F	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR047785	tRNA mnm(5)s(2)U biosynthesis bifunctional protein MnmC, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR017610	tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR006076	FAD dependent oxidoreductase	Domain

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.