9Z2O | pdb_00009z2o

CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(CTT) (No D-arm conformation)

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF25378	NSUN2 PUA domain (PUA_NSUN2)	NSUN2 PUA domain	This domain is found in RNA cytosine C(5)-methyltransferase NSUN2 from animals, multisite-specific tRNA:(cytosine-C(5))- methyltransferase (Trm4) from yeast and related proteins. NSUN2 is an RNA cytosine C5-methyltransferase that methylates cytosine ...	This domain is found in RNA cytosine C(5)-methyltransferase NSUN2 from animals, multisite-specific tRNA:(cytosine-C(5))- methyltransferase (Trm4) from yeast and related proteins. NSUN2 is an RNA cytosine C5-methyltransferase that methylates cytosine to 5-methylcytosine in various RNAs, such as tRNAs, mRNAs and some long non-coding RNAs [1,2]. Trm4 is capable of methylating cytosine to m5C at several positions in different yeast tRNAs and pre-tRNAs containing intron [3]. This domain has a detectable similarity to known PUA domains and it is predicted to adopt similar structure.	Domain
A	PF25376	NSUN2 Pre-PUA domain (Pre-PUA_NSUN2)	NSUN2 Pre-PUA domain	This domain is found in RNA cytosine C(5)-methyltransferase NSUN2 from animals, multisite-specific tRNA:(cytosine-C(5))- methyltransferase (Trm4) from yeast and related proteins. NSUN2 is an RNA cytosine C5-methyltransferase that methylates cytosine ...	This domain is found in RNA cytosine C(5)-methyltransferase NSUN2 from animals, multisite-specific tRNA:(cytosine-C(5))- methyltransferase (Trm4) from yeast and related proteins. NSUN2 is an RNA cytosine C5-methyltransferase that methylates cytosine to 5-methylcytosine in various RNAs, such as tRNAs, mRNAs and some long non-coding RNAs [1,2]. Trm4 is capable of methylating cytosine to m5C at several positions in different yeast tRNAs and pre-tRNAs containing intron [3]. This domain has detectable similarity to known pre-PUA domains and it is predicted to adopt similar structure.	Domain
A	PF01189	16S rRNA methyltransferase RsmB/F (Methyltr_RsmB-F)	16S rRNA methyltransferase RsmB/F	This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme [1,2]. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) posi ...	This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme [1,2]. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) position of cytosine 2870 (m5C2870) in 25S rRNA [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	tRNA Lys(CTT)	-	-	-
A	RNA cytosine C(5)-methyltransferase NSUN2	tRNA methyltransferase activity RNA methyltransferase activity tRNA (cytidine-N5)-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 methyltransferase activity catalytic activity RNA binding binding tRNA methyltransferase activity RNA methyltransferase activity tRNA (cytidine-N5)-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 methyltransferase activity catalytic activity RNA binding binding nucleic acid binding tRNA binding mRNA (cytidine-5-)-methyltransferase activity mRNA methyltransferase activity	developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process regulation of localization cellular localization nitrogen compound transport developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process regulation of localization cellular localization nitrogen compound transport nucleocytoplasmic transport transport regulation of mRNA export from nucleus nuclear transport mRNA transport localization intercellular transport mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport ribonucleoprotein complex localization regulation of intracellular transport regulation of ribonucleoprotein complex localization RNA transport regulation of transport regulation of RNA export from nucleus regulation of nucleobase-containing compound transport nucleic acid transport intracellular transport regulation of nucleocytoplasmic transport gene expression establishment of localization macromolecule biosynthetic process RNA export from nucleus establishment of RNA localization biosynthetic process regulation of cellular localization macromolecule localization metabolic process macromolecule metabolic process cell division RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA processing multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development tRNA modification tRNA metabolic process RNA modification tRNA processing macromolecule modification spermatid development spermatid differentiation sexual reproduction spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation male gamete generation germ cell development macromolecule methylation methylation RNA methylation tRNA methylation epithelium development epidermis development molting cycle process hair cycle animal organ development developmental maturation tissue development skin development anatomical structure maturation skin epidermis development hair follicle development molting cycle hair cycle process hair follicle maturation cellular response to stimulus regulation of cell cycle phase transition response to stimulus signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition meiotic cell cycle process intracellular signal transduction cell communication negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle regulation of cell cycle cell cycle process regulation of cell cycle process meiotic cell cycle negative regulation of cell cycle process meiotic cell cycle checkpoint signaling cell cycle checkpoint signaling negative regulation of tRNA metabolic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality tRNA decay RNA catabolic process negative regulation of metabolic process nucleobase-containing compound catabolic process regulation of gene expression tRNA stabilization regulation of tRNA metabolic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of RNA metabolic process negative regulation of tRNA catabolic process catabolic process macromolecule catabolic process regulation of tRNA stability negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of biosynthetic process negative regulation of RNA catabolic process regulation of macromolecule metabolic process regulation of catabolic process RNA stabilization regulation of tRNA catabolic process regulation of RNA stability	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen extracellular exosome extracellular vesicle extracellular organelle extracellular region vesicle extracellular membrane-bounded organelle chromatoid body cytoplasmic ribonucleoprotein granule ribonucleoprotein granule supramolecular complex nucleoplasm cytoskeleton spindle microtubule cytoskeleton

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001678	SAM-dependent methyltransferase RsmB-F/NOP2-type domain	Domain
A	IPR057286	RNA cytosine-C(5)-methyltransferase NSUN2-like, PUA domain	Domain
A	IPR049560	SAM-dependent methyltransferase RsmB-F/NOP2-type, catalytic core	Domain
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR023267	RNA (C5-cytosine) methyltransferase	Family
A	IPR023270	tRNA (C5-cytosine) methyltransferase, NCL1	Family
A	IPR057285	RNA cytosine-C(5)-methyltransferase NSUN2-like, pre-PUA domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	: Q08J23	intellectual disability, autosomal recessive 5 Dubowitz syndrome intellectual disability medulloblastoma pancreatic intraductal papillary-mucinous carcinoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm ovarian cancer progressive supranuclear palsy

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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.