NSUN4_CAEEL
ID NSUN4_CAEEL Reviewed; 465 AA.
AC Q95XR2; X5LQ37; X5LVB3;
DT 07-APR-2021, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=5-methylcytosine rRNA methyltransferase nsun-4 {ECO:0000305};
DE EC=2.1.1.- {ECO:0000255|PROSITE-ProRule:PRU01023, ECO:0000269|PubMed:33283887};
DE AltName: Full=5-methylcytosine tRNA methyltransferase nsun-4 {ECO:0000305};
DE EC=2.1.1.- {ECO:0000255|PROSITE-ProRule:PRU01023, ECO:0000269|PubMed:33283887};
DE AltName: Full=NOL1/NOP2/Sun domain family member 4 {ECO:0000312|WormBase:Y39G10AR.21a};
DE AltName: Full=RNA cytosine C(5)-methyltransferase nsun-4 {ECO:0000305};
DE AltName: Full=rRNA cytosine C(5)-methyltransferase nsun-4 {ECO:0000305};
DE AltName: Full=tRNA cytosine C(5)-methyltransferase nsun-4 {ECO:0000305};
DE Flags: Precursor;
GN Name=nsun-4 {ECO:0000312|WormBase:Y39G10AR.21a};
GN ORFNames=Y39G10AR.21 {ECO:0000312|WormBase:Y39G10AR.21a};
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239 {ECO:0000312|Proteomes:UP000001940};
RN [1] {ECO:0000312|Proteomes:UP000001940}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2 {ECO:0000312|Proteomes:UP000001940};
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
RN [2] {ECO:0000305}
RP DEVELOPMENTAL STAGE.
RX PubMed=33289480; DOI=10.7554/elife.56205;
RA Heissenberger C., Rollins J.A., Krammer T.L., Nagelreiter F., Stocker I.,
RA Wacheul L., Shpylovyi A., Tav K., Snow S., Grillari J., Rogers A.N.,
RA Lafontaine D.L., Schosserer M.;
RT "The ribosomal RNA m5C methyltransferase NSUN-1 modulates healthspan and
RT oogenesis in Caenorhabditis elegans.";
RL Elife 9:0-0(2020).
RN [3] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE,
RP AND MUTAGENESIS OF CYS-390.
RX PubMed=33283887; DOI=10.15252/embj.2020105496;
RA Navarro I.C., Tuorto F., Jordan D., Legrand C., Price J., Braukmann F.,
RA Hendrick A.G., Akay A., Kotter A., Helm M., Lyko F., Miska E.A.;
RT "Translational adaptation to heat stress is mediated by RNA 5-
RT methylcytosine in Caenorhabditis elegans.";
RL EMBO J. 0:0-0(2020).
CC -!- FUNCTION: Mitochondrial methyltransferase which methylates cytosine to
CC 5-methylcytosine (m5C) in rRNAs and tRNAs at multiple sites
CC (PubMed:33283887). May play a role in the translation of leucine and
CC proline codons (Probable). {ECO:0000269|PubMed:33283887,
CC ECO:0000305|PubMed:33283887}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a cytidine in rRNA + S-adenosyl-L-methionine = a 5-
CC methylcytidine in rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:61484, Rhea:RHEA-COMP:15836, Rhea:RHEA-COMP:15837,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000269|PubMed:33283887};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a cytidine in tRNA + S-adenosyl-L-methionine = a 5-
CC methylcytidine in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:61468, Rhea:RHEA-COMP:13670, Rhea:RHEA-COMP:15827,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000269|PubMed:33283887};
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000250|UniProtKB:Q96CB9}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=a {ECO:0000312|WormBase:Y39G10AR.21a};
CC IsoId=Q95XR2-1; Sequence=Displayed;
CC Name=b {ECO:0000312|WormBase:Y39G10AR.21b};
CC IsoId=Q95XR2-2; Sequence=VSP_060969;
CC Name=c {ECO:0000312|WormBase:Y39G10AR.21c};
CC IsoId=Q95XR2-3; Sequence=VSP_060968;
CC -!- DEVELOPMENTAL STAGE: Expression increases during the larval stages to
CC adulthood. {ECO:0000269|PubMed:33289480}.
CC -!- DISRUPTION PHENOTYPE: RNAi-mediated knockdown does not result in
CC fertility defects. {ECO:0000269|PubMed:33283887}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RsmB/NOP family. {ECO:0000255|PROSITE-ProRule:PRU01023}.
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DR EMBL; BX284601; CCD69919.1; -; Genomic_DNA.
DR EMBL; BX284601; CDO41156.1; -; Genomic_DNA.
DR EMBL; BX284601; CDO41157.1; -; Genomic_DNA.
DR RefSeq; NP_001293364.1; NM_001306435.1. [Q95XR2-2]
DR RefSeq; NP_001293365.1; NM_001306436.1. [Q95XR2-3]
DR RefSeq; NP_490958.1; NM_058557.3. [Q95XR2-1]
DR AlphaFoldDB; Q95XR2; -.
DR SMR; Q95XR2; -.
DR STRING; 6239.Y39G10AR.21; -.
DR EPD; Q95XR2; -.
DR PaxDb; Q95XR2; -.
DR PeptideAtlas; Q95XR2; -.
DR EnsemblMetazoa; Y39G10AR.21a.1; Y39G10AR.21a.1; WBGene00021476. [Q95XR2-1]
DR EnsemblMetazoa; Y39G10AR.21b.1; Y39G10AR.21b.1; WBGene00021476. [Q95XR2-2]
DR EnsemblMetazoa; Y39G10AR.21c.1; Y39G10AR.21c.1; WBGene00021476. [Q95XR2-3]
DR GeneID; 171790; -.
DR KEGG; cel:CELE_Y39G10AR.21; -.
DR UCSC; Y39G10AR.21.1; c. elegans. [Q95XR2-1]
DR CTD; 171790; -.
DR WormBase; Y39G10AR.21a; CE28981; WBGene00021476; nsun-4. [Q95XR2-1]
DR WormBase; Y39G10AR.21b; CE49666; WBGene00021476; nsun-4. [Q95XR2-2]
DR WormBase; Y39G10AR.21c; CE49707; WBGene00021476; nsun-4. [Q95XR2-3]
DR eggNOG; KOG2198; Eukaryota.
DR GeneTree; ENSGT00940000153665; -.
DR HOGENOM; CLU_041061_2_0_1; -.
DR InParanoid; Q95XR2; -.
DR OMA; FCKMCRL; -.
DR OrthoDB; 1239772at2759; -.
DR PhylomeDB; Q95XR2; -.
DR Proteomes; UP000001940; Chromosome I.
DR Bgee; WBGene00021476; Expressed in germ line (C elegans) and 4 other tissues.
DR ExpressionAtlas; Q95XR2; baseline and differential.
DR GO; GO:0005762; C:mitochondrial large ribosomal subunit; IBA:GO_Central.
DR GO; GO:0008168; F:methyltransferase activity; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0009383; F:rRNA (cytosine-C5-)-methyltransferase activity; IMP:UniProtKB.
DR GO; GO:0016428; F:tRNA (cytosine-5-)-methyltransferase activity; IMP:UniProtKB.
DR GO; GO:0001510; P:RNA methylation; IBA:GO_Central.
DR GO; GO:0031167; P:rRNA methylation; IBA:GO_Central.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR001678; MeTrfase_RsmB/NOP2.
DR InterPro; IPR023267; RCMT.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR22808; PTHR22808; 1.
DR Pfam; PF01189; Methyltr_RsmB-F; 1.
DR PRINTS; PR02008; RCMTFAMILY.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51686; SAM_MT_RSMB_NOP; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Methyltransferase; Mitochondrion; Reference proteome;
KW RNA-binding; rRNA processing; S-adenosyl-L-methionine; Transferase;
KW Transit peptide; tRNA processing.
FT TRANSIT 1..6
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 7..465
FT /note="5-methylcytosine rRNA methyltransferase nsun-4"
FT /id="PRO_0000452347"
FT REGION 106..145
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 106..128
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 390
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 260..266
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 283
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 316
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 335
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT VAR_SEQ 1..427
FT /note="Missing (in isoform c)"
FT /evidence="ECO:0000305"
FT /id="VSP_060968"
FT VAR_SEQ 1..89
FT /note="Missing (in isoform b)"
FT /evidence="ECO:0000305"
FT /id="VSP_060969"
FT MUTAGEN 390
FT /note="C->A: In mj457; viable and produces viable progeny.
FT Reduces body length. Reduces mitochondrial tRNA and rRNA
FT methylation state. Increases the reduction in body length,
FT and at 25 degrees Celsius reduces the number of progeny in
FT a nsun-1 (mj473), nsun-2 (mj458) and nsun-5 (tm3898) mutant
FT background. Abolishes the methylation of carbon-5 cysteines
FT and its metabolic derivative 2'-O-methyl-5-
FT hydroxymethylcytosine in RNA in a nsun-1 (mj473), nsun-2
FT (mj458) and nsun-5 (tm3898) mutant background."
FT /evidence="ECO:0000269|PubMed:33283887"
SQ SEQUENCE 465 AA; 51520 MW; B42CD0CCAE0D1CD2 CRC64;
MSCLRQSSQS FYFTQIRWKT VKFKTKIAKT KPLKTPSAQA LDHFDFYYGP LFGKKWPSIR
LGLLSPNRYL AVMNTMSRNW QAHDEILSDM GAKDLLASIR GKAEDQAIET KRKSVEEKAN
RETQKVKHEI SNPSTSTNTE DSEPDEAIFR SAAGLGEFRA SAGELSSGSL QMGLGQSNQN
KNVEITGFEG EGVRIPKRDH FFYYPQALHV RSFDRAVLLD FPAPMKDEVG VPSYWLLDGG
SLLPVLALGL QKDDSLLDMC AAPGGKSLLA ALSNLPSKIV CNDFKLARLG QLKRALMTYV
PEDSETIDKF VLKRKDASDV KTWDEFEAYD KVLVDVPCST DRLSVSTDDG NLFSTGSTQQ
RLDLPVLQTK ILVNALRSVK VGGSVVYSTC TLSPSQNEAV VENAVAVVRN DFGIVTVEES
LHQLVSHMTS SGLYRFHDTP LGALVVPFLP SNFGPMYICK LTRLQ
