3KU1 | pdb_00003ku1

Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA (m1A22) methyltransferase, in complex with S-adenosyl-L-methionine

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)
A	SCOP2 Family	m1A22 tRNA Methyltransferase TrmK-like	8046488	4005114	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090769	3000118	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090769	3000118	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090769	3000118	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090769	3000118	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090769	3000118	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090769	3000118	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090769	3000118	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090769	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)
A	TrmK	e3ku1A1	A: alpha bundles	X: Long alpha-hairpin	H: Helical hairpin in putative tRNA methyltransferase (From Topology)	T: Helical hairpin in putative tRNA methyltransferase	F: TrmK	ECOD (1.6)
A	Methyltransf_18	e3ku1A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_18	ECOD (1.6)
B	TrmK	e3ku1B2	A: alpha bundles	X: Long alpha-hairpin	H: Helical hairpin in putative tRNA methyltransferase (From Topology)	T: Helical hairpin in putative tRNA methyltransferase	F: TrmK	ECOD (1.6)
B	Methyltransf_18	e3ku1B1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_18	ECOD (1.6)
D	TrmK	e3ku1D2	A: alpha bundles	X: Long alpha-hairpin	H: Helical hairpin in putative tRNA methyltransferase (From Topology)	T: Helical hairpin in putative tRNA methyltransferase	F: TrmK	ECOD (1.6)
D	Methyltransf_18	e3ku1D1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_18	ECOD (1.6)
G	TrmK	e3ku1G2	A: alpha bundles	X: Long alpha-hairpin	H: Helical hairpin in putative tRNA methyltransferase (From Topology)	T: Helical hairpin in putative tRNA methyltransferase	F: TrmK	ECOD (1.6)
G	Methyltransf_18	e3ku1G1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_18	ECOD (1.6)
H	TrmK	e3ku1H2	A: alpha bundles	X: Long alpha-hairpin	H: Helical hairpin in putative tRNA methyltransferase (From Topology)	T: Helical hairpin in putative tRNA methyltransferase	F: TrmK	ECOD (1.6)
H	Methyltransf_18	e3ku1H1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_18	ECOD (1.6)
F	TrmK	e3ku1F1	A: alpha bundles	X: Long alpha-hairpin	H: Helical hairpin in putative tRNA methyltransferase (From Topology)	T: Helical hairpin in putative tRNA methyltransferase	F: TrmK	ECOD (1.6)
F	Methyltransf_18	e3ku1F2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_18	ECOD (1.6)
E	TrmK	e3ku1E2	A: alpha bundles	X: Long alpha-hairpin	H: Helical hairpin in putative tRNA methyltransferase (From Topology)	T: Helical hairpin in putative tRNA methyltransferase	F: TrmK	ECOD (1.6)
E	Methyltransf_18	e3ku1E1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_18	ECOD (1.6)
C	TrmK	e3ku1C2	A: alpha bundles	X: Long alpha-hairpin	H: Helical hairpin in putative tRNA methyltransferase (From Topology)	T: Helical hairpin in putative tRNA methyltransferase	F: TrmK	ECOD (1.6)
C	Methyltransf_18	e3ku1C1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_18	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A	1.10.287.1890	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		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	1.10.287.1890	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		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	1.10.287.1890	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
G	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
G	1.10.287.1890	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
H	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
H	1.10.287.1890	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
F	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
F	1.10.287.1890	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		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	1.10.287.1890	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		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	1.10.287.1890	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		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, G, H	PF04816	tRNA (adenine(22)-N(1))-methyltransferase (TrmK)	tRNA (adenine(22)-N(1))-methyltransferase	-	Family

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, G, H	SAM-dependent methyltransferase	tRNA methyltransferase activity RNA methyltransferase activity tRNA (adenine(22)-N1)-methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity tRNA (adenine) methyltransferase activity methyltransferase activity catalytic activity	methylation metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006901	tRNA methyltransferase TrmK	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.