4BY9 | pdb_00004by9

The structure of the Box CD enzyme reveals regulation of rRNA methylation

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)
M	SCOP2B Superfamily	L30e-like	8033057	3001739	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	L30e-like	8033057	3001739	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	L30e-like	8033057	3001739	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	L30e-like	8033057	3001739	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063654	3000118	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063654	3000118	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063654	3000118	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063654	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)
L		e4by9L2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F:	ECOD (v294.1)
L	Molybdopterin	e4by9L3	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: Molybdopterin	ECOD (v294.1)
I	HTH_24	e4by9I3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: HTH_24	ECOD (v294.1)
I	Molybdopterin	e4by9I2	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: Molybdopterin	ECOD (v294.1)
F		e4by9F2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F:	ECOD (v294.1)
F	Molybdopterin	e4by9F3	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: Molybdopterin	ECOD (v294.1)
C	HTH_24	e4by9C3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: HTH_24	ECOD (v294.1)
C	Molybdopterin	e4by9C2	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: Molybdopterin	ECOD (v294.1)
M		e4by9M1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F:	ECOD (v294.1)
J		e4by9J1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F:	ECOD (v294.1)
G		e4by9G1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F:	ECOD (v294.1)
D		e4by9D1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F:	ECOD (v294.1)
N		e4by9N1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F:	ECOD (v294.1)
K		e4by9K1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F:	ECOD (v294.1)
H		e4by9H1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F:	ECOD (v294.1)
E		e4by9E1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.30.420.220	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
L	1.10.287.4070	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
L	1.10.246.90	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
I	3.30.420.220	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
I	1.10.287.4070	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
I	1.10.246.90	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
F	3.30.420.220	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
F	1.10.287.4070	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
F	1.10.246.90	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
C	3.30.420.220	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	1.10.287.4070	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
C	1.10.246.90	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
M	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
J	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
G	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
D	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
N	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
N	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
K	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
K	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
H	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	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)
E	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F, I, L	PF21572	Archaeal Nop5/56-rel, N-terminal domain (Nop5_56-rel_N_Arc)	Archaeal Nop5/56-rel, N-terminal domain	This domain is found at the N-terminal end of a group of archaeal proteins, including Uncharacterized NOP5 family protein MJ0694 from Methanocaldococcus jannaschii. This domain interacts with fibrillarin, the other subunit of a complex that is critic ...	This domain is found at the N-terminal end of a group of archaeal proteins, including Uncharacterized NOP5 family protein MJ0694 from Methanocaldococcus jannaschii. This domain interacts with fibrillarin, the other subunit of a complex that is critical to modify and process ribosomal RNAs [1-5]. This domain shows a highly conserved folded structure despite low sequence similarity among homologs. It shows four beta-sheets surrounded by four alpha- helices [6] and is found associated with Pfam:PF01798.	Domain
C, F, I, L	PF01798	snoRNA binding domain, fibrillarin (Nop)	snoRNA binding domain, fibrillarin	-	Family
D, G, J, M	PF01248	Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae)	Ribosomal protein L7Ae/L30e/S12e/Gadd45 family	This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD11 ...	This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118 [1].	Domain
E, H, K, N	PF01269	Fibrillarin (Fibrillarin)	Fibrillarin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I, L	NOP5/NOP56 RELATED PROTEIN	RNA binding binding snoRNA binding nucleic acid binding	-	box C/D methylation guide snoRNP complex protein-containing complex sno(s)RNA-containing ribonucleoprotein complex ribonucleoprotein complex box C/D RNP complex
D, G, J, M	50S RIBOSOMAL PROTEIN L7AE	RNA binding binding rRNA binding nucleic acid binding tRNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity, acting on a tRNA hydrolase activity nuclease activity hydrolase activity, acting on ester bonds RNA binding binding rRNA binding nucleic acid binding tRNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity, acting on a tRNA hydrolase activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity ribonuclease P activity catalytic activity structural molecule activity structural constituent of ribosome	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 biosynthetic process tRNA processing RNA 5'-end processing metabolic process 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 biosynthetic process tRNA processing RNA 5'-end processing metabolic process cellular process macromolecule metabolic process RNA processing tRNA 5'-leader removal tRNA 5'-end processing ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis rRNA metabolic process protein metabolic process translation protein biosynthetic process	protein-containing complex ribonucleoprotein complex cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle ribosome
E, H, K, N	FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE	catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein-glutamine N-methyltransferase activity transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity N-methyltransferase activity protein methyltransferase activity histone modifying activity methyltransferase activity catalytic activity histone H2A methyltransferase activity histone H2AQ104 methyltransferase activity RNA binding catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein-glutamine N-methyltransferase activity transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity N-methyltransferase activity protein methyltransferase activity histone modifying activity methyltransferase activity catalytic activity histone H2A methyltransferase activity histone H2AQ104 methyltransferase activity RNA binding binding nucleic acid binding RNA methyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a rRNA	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 biosynthetic process tRNA processing metabolic process cellular process 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 biosynthetic process tRNA processing metabolic process cellular process macromolecule metabolic process RNA processing sno(s)RNA processing box C/D sno(s)RNA metabolic process box C/D sno(s)RNA processing sno(s)RNA 3'-end processing sno(s)RNA metabolic process box C/D sno(s)RNA 3'-end processing RNA 3'-end processing	-
O [auth W], P [auth X], Q [auth Y], R [auth Z]	5'-R(UPCPGPCPCPCPAPUPCPAP*CP)-3'	-	-	-
A, B	SSR26	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I, L	IPR042239	Nop, C-terminal domain	Homologous Superfamily
C, F, I, L	IPR036070	Nop domain superfamily	Homologous Superfamily
C, F, I, L	IPR045056	Nucleolar protein Nop56/Nop58	Family
C, F, I, L	IPR002687	Nop domain	Domain
C, F, I, L	IPR029012	Helix hairpin bin domain superfamily	Homologous Superfamily
C, F, I, L	IPR048896	Nop5/56-related, N-terminal domain	Domain
C, F, I, L	IPR012976	NOSIC	Domain
C, F, I, L	IPR047099	Nop5, N-terminal domain superfamily	Homologous Superfamily
D, G, J, M	IPR050257	Large ribosomal subunit protein eL8/uL1-like	Family
D, G, J, M	IPR004038	Ribosomal protein eL8/eL30/eS12/Gadd45	Domain
D, G, J, M	IPR022481	Large ribosomal subunit protein eL8, archaea	Family
D, G, J, M	IPR004037	Large ribosomal subunit protein eL8-like, conserved site	Conserved Site
D, G, J, M	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily
D, G, J, M	IPR018492	Ribosomal protein eL8/Nhp2 family	Family
E, H, K, N	IPR000692	rRNA 2'-O-methyltransferase fibrillarin-like	Family
E, H, K, N	IPR020813	Fibrillarin, conserved site	Conserved Site
E, H, K, N	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily