1GZ0 | pdb_00001gz0

23S RIBOSOMAL RNA G2251 2'O-METHYLTRANSFERASE RLMB

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)
H	d1gz0h1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	SpoU-like RNA 2'-O ribose methyltransferase	RlmB, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d1gz0h2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	L30e-like	RNA 2'-O ribose methyltransferase substrate binding domain	RlmB, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d1gz0h3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d1gz0g1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	SpoU-like RNA 2'-O ribose methyltransferase	RlmB, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1gz0f1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	SpoU-like RNA 2'-O ribose methyltransferase	RlmB, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1gz0f2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	L30e-like	RNA 2'-O ribose methyltransferase substrate binding domain	RlmB, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1gz0f3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1gz0e1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	SpoU-like RNA 2'-O ribose methyltransferase	RlmB, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1gz0d1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	SpoU-like RNA 2'-O ribose methyltransferase	RlmB, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1gz0d2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	L30e-like	RNA 2'-O ribose methyltransferase substrate binding domain	RlmB, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1gz0d3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1gz0c1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	SpoU-like RNA 2'-O ribose methyltransferase	RlmB, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1gz0c2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	L30e-like	RNA 2'-O ribose methyltransferase substrate binding domain	RlmB, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1gz0b1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	SpoU-like RNA 2'-O ribose methyltransferase	RlmB, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1gz0b2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	L30e-like	RNA 2'-O ribose methyltransferase substrate binding domain	RlmB, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1gz0b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1gz0a1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	SpoU-like RNA 2'-O ribose methyltransferase	RlmB, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1gz0a2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	L30e-like	RNA 2'-O ribose methyltransferase substrate binding domain	RlmB, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	alpha/beta knot	8042308	3001122	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	L30e-like	8042309	3001739	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	alpha/beta knot	8042308	3001122	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	alpha/beta knot	8042308	3001122	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	L30e-like	8042309	3001739	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	alpha/beta knot	8042308	3001122	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	alpha/beta knot	8042308	3001122	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	L30e-like	8042309	3001739	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	alpha/beta knot	8042308	3001122	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	L30e-like	8042309	3001739	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	alpha/beta knot	8042308	3001122	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	L30e-like	8042309	3001739	SCOP2B (2022-06-29)
A	SCOP2 Family	SpoU-like RNA 2'-O ribose methyltransferase	8029929	4002340	SCOP2 (2022-06-29)
A	SCOP2 Family	RNA 2'-O ribose methyltransferase substrate binding domain	8029930	4002711	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	alpha/beta knot	8042308	3001122	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	L30e-like	8042309	3001739	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	Ribonuc_L-PSP	e1gz0H1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Ribonuc_L-PSP	ECOD (v294.1)
H	RecU	e1gz0H2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (v294.1)
G	RecU	e1gz0G1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (v294.1)
F	Ribonuc_L-PSP	e1gz0F1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Ribonuc_L-PSP	ECOD (v294.1)
F	RecU	e1gz0F2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (v294.1)
E	RecU	e1gz0E1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (v294.1)
D	Ribonuc_L-PSP	e1gz0D1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Ribonuc_L-PSP	ECOD (v294.1)
D	RecU	e1gz0D2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (v294.1)
C	Ribonuc_L-PSP	e1gz0C1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Ribonuc_L-PSP	ECOD (v294.1)
C	RecU	e1gz0C2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (v294.1)
B	Ribonuc_L-PSP	e1gz0B1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Ribonuc_L-PSP	ECOD (v294.1)
B	RecU	e1gz0B2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (v294.1)
A	SpoU_sub_bind	e1gz0A1	A: a+b three layers	X: FwdE/GAPDH domain-like	H: L30e-like	T: L30e-like	F: SpoU_sub_bind	ECOD (v294.1)
A	SpoU_methylase	e1gz0A2	A: a/b three-layered sandwiches	X: alpha/beta knot	H: alpha/beta knot	T: alpha/beta knot	F: SpoU_methylase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	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)
G	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
F	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	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)
E	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
D	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	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)
C	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	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)
B	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	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)
A	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
A	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	PF08032	RNA 2'-O ribose methyltransferase substrate binding (SpoU_sub_bind)	RNA 2'-O ribose methyltransferase substrate binding	This domain is a RNA 2'-O ribose methyltransferase substrate binding domain.	Domain
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	HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH	RNA binding binding nucleic acid binding RNA methyltransferase activity O-methyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity catalytic activity, acting on a rRNA S-adenosylmethionine-dependent methyltransferase activity rRNA (guanosine-2'-O-ribose)-methyltransferase activity methyltransferase activity RNA binding binding nucleic acid binding RNA methyltransferase activity O-methyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity catalytic activity, acting on a rRNA S-adenosylmethionine-dependent methyltransferase activity rRNA (guanosine-2'-O-ribose)-methyltransferase activity methyltransferase activity catalytic activity rRNA (guanine) methyltransferase activity RNA 2'-O-methyltransferase activity	ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

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	IPR004441	RNA methyltransferase TrmH	Family
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	IPR024915	23S rRNA (guanosine-2-O-)-methyltransferase RlmB	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013123	RNA 2-O ribose methyltransferase, substrate binding	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.