1IXK

Crystal Structure Analysis of Methyltransferase Homolog Protein from Pyrococcus Horikoshii

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	d1ixka_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	NOL1/NOP2/sun	Hypothetical methyltransferase PH1374	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	NOL1/NOP2/sun	8023568	4001157	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8035948	3000118	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RNA-binding domain, RBD	8090692	3000110	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)
A	Methyltr_RsmF_N	e1ixkA2	A: a+b two layers	X: Alpha-beta plaits	H: NOL1/NOP2/sun N-terminal ferredoxin-like domain (From Topology)	T: NOL1/NOP2/sun N-terminal ferredoxin-like domain	F: Methyltr_RsmF_N	ECOD (1.6)
A	Methyltr_RsmB-F_1	e1ixkA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltr_RsmB-F_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.1170	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Sun protein	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF17125	N-terminal domain of 16S rRNA methyltransferase RsmF (Methyltr_RsmF_N)	N-terminal domain of 16S rRNA methyltransferase RsmF	This is the N-terminal domain of the RsmF methyl transferase. RsmF is a multi-site-specific methyltransferase that is responsible for the synthesis of three modifications on cytidines in 16S ribosomal RNA. The N-terminus is critical for stabilising t ...	This is the N-terminal domain of the RsmF methyl transferase. RsmF is a multi-site-specific methyltransferase that is responsible for the synthesis of three modifications on cytidines in 16S ribosomal RNA. The N-terminus is critical for stabilising the catalytic core of the enzyme [1]. It has a ferredoxin-like fold.	Domain
A	PF01189	16S rRNA methyltransferase RsmB/F (Methyltr_RsmB-F)	16S rRNA methyltransferase RsmB/F	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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-5-)-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-5-)-methyltransferase activity methyltransferase activity catalytic activity RNA binding binding nucleic acid binding	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 tRNA processing tRNA modification macromolecule methylation tRNA metabolic process RNA modification methylation macromolecule modification RNA methylation tRNA methylation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR031341	Ribosomal RNA small subunit methyltransferase F, N-terminal	Domain
A	IPR018314	RsmB/NOL1/NOP2-like, conserved site	Conserved Site
A	IPR001678	SAM-dependent methyltransferase RsmB-F/NOP2-type domain	Domain
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR049560	SAM-dependent methyltransferase RsmB-F/NOP2-type, catalytic core	Domain
A	IPR023267	RNA (C5-cytosine) methyltransferase	Family
A	IPR011023	Nop2p	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.