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Protein

5-methylcytosine rRNA methyltransferase NSUN4

Gene

NSUN4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in mitochondrial ribosome assembly. 5-methylcytosine rRNA methyltransferase that probably is involved in mitochondrial ribosome small subunit (SSU) maturation by methylation of mitochondrial 12S rRNA; the function is independent of MTERFD2/MTERF4 and assembled mitochondrial ribosome large subunit (LSU). Targeted to LSU by MTERFD2/MTERF4 and probably is involved in a final step in ribosome biogenesis to ensure that SSU and LSU are assembled. In vitro can methylate 16S rRNA of the LSU; the methylation is enhanced by MTERFD/MTERF4.2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei237S-adenosyl-L-methioninePROSITE-ProRule annotation1 Publication1
Binding sitei255S-adenosyl-L-methioninePROSITE-ProRule annotation1 Publication1
Active sitei310NucleophilePROSITE-ProRule annotation1 Publication1

GO - Molecular functioni

  • methyltransferase activity Source: UniProtKB
  • rRNA binding Source: UniProtKB-KW

GO - Biological processi

  • rRNA methylation Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Keywords - Ligandi

RNA-binding, rRNA-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciZFISH:ENSG00000117481-MONOMER.
ReactomeiR-HSA-6793080. rRNA modification in the mitochondrion.

Names & Taxonomyi

Protein namesi
Recommended name:
5-methylcytosine rRNA methyltransferase NSUN4 (EC:2.1.1.-)
Alternative name(s):
NOL1/NOP2/Sun domain family member 4
Gene namesi
Name:NSUN4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:31802. NSUN4.

Subcellular locationi

GO - Cellular componenti

  • mitochondrial large ribosomal subunit Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi65V → R: Disrupts complex with MTERFD2; when associated with A-136, R-139 and A-141. 1 Publication1
Mutagenesisi136R → A: Disrupts complex with MTERFD2; when associated with R-65, R-139 and A-141. 1 Publication1
Mutagenesisi139I → R: Disrupts complex with MTERFD2; when associated with R-65, A-136, and A-141. 1 Publication1
Mutagenesisi141R → A: Disrupts complex with MTERFD2; when associated with R-65, A-136 and R-139. 1 Publication1

Organism-specific databases

OpenTargetsiENSG00000117481.
PharmGKBiPA134953046.

Polymorphism and mutation databases

BioMutaiNSUN4.
DMDMi152125805.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 25Mitochondrion1 PublicationAdd BLAST25
ChainiPRO_000028923426 – 3845-methylcytosine rRNA methyltransferase NSUN4Add BLAST359

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei206PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ96CB9.
MaxQBiQ96CB9.
PaxDbiQ96CB9.
PeptideAtlasiQ96CB9.
PRIDEiQ96CB9.

PTM databases

iPTMnetiQ96CB9.
PhosphoSitePlusiQ96CB9.

Expressioni

Gene expression databases

BgeeiENSG00000117481.
CleanExiHS_NSUN4.
ExpressionAtlasiQ96CB9. baseline and differential.
GenevisibleiQ96CB9. HS.

Organism-specific databases

HPAiHPA027958.
HPA028489.

Interactioni

Protein-protein interaction databases

BioGridi132288. 29 interactors.
DIPiDIP-58104N.
IntActiQ96CB9. 13 interactors.
MINTiMINT-1474456.
STRINGi9606.ENSP00000419740.

Structurei

Secondary structure

1384
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi40 – 56Combined sources17
Helixi57 – 59Combined sources3
Helixi60 – 67Combined sources8
Beta strandi74 – 77Combined sources4
Helixi79 – 81Combined sources3
Helixi83 – 92Combined sources10
Helixi98 – 104Combined sources7
Turni105 – 107Combined sources3
Helixi121 – 124Combined sources4
Beta strandi131 – 133Combined sources3
Beta strandi151 – 158Combined sources8
Helixi160 – 162Combined sources3
Helixi163 – 169Combined sources7
Beta strandi175 – 181Combined sources7
Helixi186 – 193Combined sources8
Beta strandi197 – 203Combined sources7
Helixi207 – 220Combined sources14
Turni223 – 227Combined sources5
Beta strandi228 – 234Combined sources7
Helixi238 – 240Combined sources3
Helixi241 – 244Combined sources4
Beta strandi249 – 255Combined sources7
Helixi261 – 264Combined sources4
Helixi275 – 277Combined sources3
Helixi278 – 282Combined sources5
Helixi284 – 297Combined sources14
Beta strandi299 – 310Combined sources12
Turni314 – 317Combined sources4
Helixi318 – 332Combined sources15
Beta strandi336 – 338Combined sources3
Helixi342 – 348Combined sources7
Turni349 – 351Combined sources3
Beta strandi359 – 365Combined sources7
Beta strandi375 – 382Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4FP9X-ray2.90A/C/D/F26-384[»]
4FZVX-ray2.00A26-384[»]
ProteinModelPortaliQ96CB9.
SMRiQ96CB9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni181 – 187S-adenosyl-L-methionine binding7

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family.PROSITE-ProRule annotation

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG2198. Eukaryota.
COG0144. LUCA.
GeneTreeiENSGT00660000095341.
HOGENOMiHOG000017426.
HOVERGENiHBG106892.
InParanoidiQ96CB9.
PhylomeDBiQ96CB9.
TreeFamiTF321304.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR001678. MeTrfase_RsmB/NOP2.
IPR023267. RCMT.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01189. Methyltr_RsmB-F. 1 hit.
[Graphical view]
PRINTSiPR02008. RCMTFAMILY.
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS51686. SAM_MT_RSMB_NOP. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q96CB9-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAALTLRGVR ELLKRVDLAT VPRRHRYKKK WAATEPKFPA VRLALQNFDM
60 70 80 90 100
TYSVQFGDLW PSIRVSLLSE QKYGALVNNF AAWDHVSAKL EQLSAKDFVN
110 120 130 140 150
EAISHWELQS EGGQSAAPSP ASWACSPNLR CFTFDRGDIS RFPPARPGSL
160 170 180 190 200
GVMEYYLMDA ASLLPVLALG LQPGDIVLDL CAAPGGKTLA LLQTGCCRNL
210 220 230 240 250
AANDLSPSRI ARLQKILHSY VPEEIRDGNQ VRVTSWDGRK WGELEGDTYD
260 270 280 290 300
RVLVDVPCTT DRHSLHEEEN NIFKRSRKKE RQILPVLQVQ LLAAGLLATK
310 320 330 340 350
PGGHVVYSTC SLSHLQNEYV VQGAIELLAN QYSIQVQVED LTHFRRVFMD
360 370 380
TFCFFSSCQV GELVIPNLMA NFGPMYFCKM RRLT
Length:384
Mass (Da):43,089
Last modified:May 29, 2007 - v2
Checksum:i4D83B6D55D65C27F
GO
Isoform 2 (identifier: Q96CB9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     147-384: Missing.

Note: No experimental confirmation available.
Show »
Length:146
Mass (Da):16,507
Checksum:iE49A839AA5937FB5
GO
Isoform 3 (identifier: Q96CB9-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-198: Missing.
     199-219: NLAANDLSPSRIARLQKILHS → MLPPCCLFWPSACSLGTSCLT

Note: No experimental confirmation available.
Show »
Length:186
Mass (Da):21,240
Checksum:i4186007A46B086CD
GO
Isoform 4 (identifier: Q96CB9-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-49: Missing.

Note: No experimental confirmation available.
Show »
Length:335
Mass (Da):37,374
Checksum:i85AACD29E9DDB7D7
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti282Q → R in BAG51912 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03260651T → A.2 PublicationsCorresponds to variant rs3737744dbSNPEnsembl.1
Natural variantiVAR_032607128N → K.Corresponds to variant rs17102152dbSNPEnsembl.1
Natural variantiVAR_032608325I → T.Corresponds to variant rs13374337dbSNPEnsembl.1
Natural variantiVAR_032609365I → V.1 PublicationCorresponds to variant rs9865dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0259711 – 198Missing in isoform 3. 1 PublicationAdd BLAST198
Alternative sequenceiVSP_0450531 – 49Missing in isoform 4. 1 PublicationAdd BLAST49
Alternative sequenceiVSP_025972147 – 384Missing in isoform 2. 1 PublicationAdd BLAST238
Alternative sequenceiVSP_025973199 – 219NLAAN…KILHS → MLPPCCLFWPSACSLGTSCL T in isoform 3. 1 PublicationAdd BLAST21

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK021577 mRNA. Translation: BAB13847.1.
AK057420 mRNA. Translation: BAG51912.1.
AK291741 mRNA. Translation: BAF84430.1.
AK295003 mRNA. Translation: BAG58065.1.
AL122001 Genomic DNA. Translation: CAI21962.1.
CH471059 Genomic DNA. Translation: EAX06917.1.
BC014441 mRNA. Translation: AAH14441.1.
BC016907 mRNA. Translation: AAH16907.1.
CCDSiCCDS534.1. [Q96CB9-1]
CCDS57996.1. [Q96CB9-4]
RefSeqiNP_001243056.1. NM_001256127.1. [Q96CB9-4]
NP_001243057.1. NM_001256128.1. [Q96CB9-4]
NP_950245.2. NM_199044.3. [Q96CB9-1]
UniGeneiHs.163424.

Genome annotation databases

EnsembliENST00000474844; ENSP00000419740; ENSG00000117481. [Q96CB9-1]
ENST00000537428; ENSP00000437758; ENSG00000117481. [Q96CB9-4]
GeneIDi387338.
KEGGihsa:387338.
UCSCiuc001cpr.3. human. [Q96CB9-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK021577 mRNA. Translation: BAB13847.1.
AK057420 mRNA. Translation: BAG51912.1.
AK291741 mRNA. Translation: BAF84430.1.
AK295003 mRNA. Translation: BAG58065.1.
AL122001 Genomic DNA. Translation: CAI21962.1.
CH471059 Genomic DNA. Translation: EAX06917.1.
BC014441 mRNA. Translation: AAH14441.1.
BC016907 mRNA. Translation: AAH16907.1.
CCDSiCCDS534.1. [Q96CB9-1]
CCDS57996.1. [Q96CB9-4]
RefSeqiNP_001243056.1. NM_001256127.1. [Q96CB9-4]
NP_001243057.1. NM_001256128.1. [Q96CB9-4]
NP_950245.2. NM_199044.3. [Q96CB9-1]
UniGeneiHs.163424.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4FP9X-ray2.90A/C/D/F26-384[»]
4FZVX-ray2.00A26-384[»]
ProteinModelPortaliQ96CB9.
SMRiQ96CB9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi132288. 29 interactors.
DIPiDIP-58104N.
IntActiQ96CB9. 13 interactors.
MINTiMINT-1474456.
STRINGi9606.ENSP00000419740.

PTM databases

iPTMnetiQ96CB9.
PhosphoSitePlusiQ96CB9.

Polymorphism and mutation databases

BioMutaiNSUN4.
DMDMi152125805.

Proteomic databases

EPDiQ96CB9.
MaxQBiQ96CB9.
PaxDbiQ96CB9.
PeptideAtlasiQ96CB9.
PRIDEiQ96CB9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000474844; ENSP00000419740; ENSG00000117481. [Q96CB9-1]
ENST00000537428; ENSP00000437758; ENSG00000117481. [Q96CB9-4]
GeneIDi387338.
KEGGihsa:387338.
UCSCiuc001cpr.3. human. [Q96CB9-1]

Organism-specific databases

CTDi387338.
GeneCardsiNSUN4.
HGNCiHGNC:31802. NSUN4.
HPAiHPA027958.
HPA028489.
MIMi615394. gene.
neXtProtiNX_Q96CB9.
OpenTargetsiENSG00000117481.
PharmGKBiPA134953046.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2198. Eukaryota.
COG0144. LUCA.
GeneTreeiENSGT00660000095341.
HOGENOMiHOG000017426.
HOVERGENiHBG106892.
InParanoidiQ96CB9.
PhylomeDBiQ96CB9.
TreeFamiTF321304.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000117481-MONOMER.
ReactomeiR-HSA-6793080. rRNA modification in the mitochondrion.

Miscellaneous databases

GenomeRNAii387338.
PROiQ96CB9.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000117481.
CleanExiHS_NSUN4.
ExpressionAtlasiQ96CB9. baseline and differential.
GenevisibleiQ96CB9. HS.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR001678. MeTrfase_RsmB/NOP2.
IPR023267. RCMT.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01189. Methyltr_RsmB-F. 1 hit.
[Graphical view]
PRINTSiPR02008. RCMTFAMILY.
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS51686. SAM_MT_RSMB_NOP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNSUN4_HUMAN
AccessioniPrimary (citable) accession number: Q96CB9
Secondary accession number(s): A8K6S6
, B3KQ50, B4DHA4, Q5TDF7, Q96AN8, Q9HAJ8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 29, 2007
Last sequence update: May 29, 2007
Last modified: November 30, 2016
This is version 110 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.