4KGN | pdb_00004kgn

Crystal structure of a tRNA (cytidine(34)-2'-O)-methyltransferase bound to S-adenosyl homocysteine

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	d4kgna_	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	automated matches	automated matches	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
B	d4kgnb_	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	automated matches	automated matches	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
C	d4kgnc1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	automated matches	automated matches	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
C	d4kgnc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
D	d4kgnd1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	automated matches	automated matches	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
D	d4kgnd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
E	d4kgne_	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	automated matches	automated matches	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
G	d4kgng_	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	automated matches	automated matches	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
H	d4kgnh_	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	automated matches	automated matches	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
F	d4kgnf1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	automated matches	automated matches	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)
F	d4kgnf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Burkholderia pseudomallei 1710b ) [TaxId: 320372 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	alpha/beta knot	8099410	3001122	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	alpha/beta knot	8099410	3001122	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	alpha/beta knot	8099410	3001122	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	alpha/beta knot	8099410	3001122	SCOP2B (2022-06-29)
E	SCOP2 Family	SpoU-like RNA 2'-O ribose methyltransferase	8099409	4002340	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	alpha/beta knot	8099410	3001122	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	alpha/beta knot	8099410	3001122	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	alpha/beta knot	8099410	3001122	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	alpha/beta knot	8099410	3001122	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	SpoU_methylase	e4kgnA1	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: SpoU_methylase	ECOD (1.6)
B	SpoU_methylase	e4kgnB2	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: SpoU_methylase	ECOD (1.6)
C	SpoU_methylase	e4kgnC2	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: SpoU_methylase	ECOD (1.6)
D	SpoU_methylase	e4kgnD1	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: SpoU_methylase	ECOD (1.6)
E	SpoU_methylase	e4kgnE2	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: SpoU_methylase	ECOD (1.6)
G	SpoU_methylase	e4kgnG2	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: SpoU_methylase	ECOD (1.6)
H	SpoU_methylase	e4kgnH2	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: SpoU_methylase	ECOD (1.6)
F	SpoU_methylase	e4kgnF1	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: SpoU_methylase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
B	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
C	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
D	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
E	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
G	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
H	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
F	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	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	PF00588	SpoU rRNA Methylase family (SpoU_methylase)	SpoU rRNA Methylase family	-	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	tRNA (cytidine(34)-2'-O)-methyltransferase	tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA tRNA (cytidine) methyltransferase activity 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 (cytidine(34)-2'-O)-methyltransferase activity methyltransferase activity catalytic activity RNA binding binding tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA tRNA (cytidine) methyltransferase activity 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 (cytidine(34)-2'-O)-methyltransferase activity methyltransferase activity catalytic activity RNA binding binding nucleic acid binding tRNA (5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase activity tRNA (uridine) methyltransferase activity identical protein binding protein binding	RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing wobble position uridine ribose methylation tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing wobble position uridine ribose methylation tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation wobble position ribose methylation tRNA metabolic process tRNA nucleoside ribose methylation RNA modification biosynthetic process methylation macromolecule modification metabolic process cellular process macromolecule metabolic process RNA methylation tRNA methylation wobble position cytosine ribose methylation	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, G, H	IPR001537	tRNA/rRNA methyltransferase, SpoU type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029026	tRNA (guanine-N1-)-methyltransferase, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029028	Alpha/beta knot methyltransferases	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR016914	tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmL	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.