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Protein

5-methylcytosine rRNA methyltransferase NSUN4

Gene

NSUN4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

GO - Biological processi

Keywordsi

Molecular functionMethyltransferase, RNA-binding, rRNA-binding, Transferase
Biological processRibosome biogenesis, rRNA processing
LigandS-adenosyl-L-methionine

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000117481.10
HGNCiHGNC:31802 NSUN4
MIMi615394 gene
neXtProtiNX_Q96CB9

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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 – 25Mitochondrion2 PublicationsAdd 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
ProteomicsDBi76175
76176 [Q96CB9-2]
76177 [Q96CB9-3]

PTM databases

iPTMnetiQ96CB9
PhosphoSitePlusiQ96CB9

Expressioni

Gene expression databases

BgeeiENSG00000117481 Expressed in 199 organ(s), highest expression level in testis
CleanExiHS_NSUN4
ExpressionAtlasiQ96CB9 baseline and differential
GenevisibleiQ96CB9 HS

Organism-specific databases

HPAiHPA028489

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
MTERF4Q7Z6M47EBI-16012886,EBI-948435

Protein-protein interaction databases

BioGridi132288, 29 interactors
DIPiDIP-58104N
IntActiQ96CB9, 15 interactors
MINTiQ96CB9
STRINGi9606.ENSP00000419740

Structurei

Secondary structure

1384
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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
KOiK21970
PhylomeDBiQ96CB9
TreeFamiTF321304

Family and domain databases

InterProiView protein in InterPro
IPR001678 MeTrfase_RsmB/NOP2
IPR023267 RCMT
IPR029063 SAM-dependent_MTases
PfamiView protein in Pfam
PF01189 Methyltr_RsmB-F, 1 hit
PRINTSiPR02008 RCMTFAMILY
SUPFAMiSSF53335 SSF53335, 1 hit
PROSITEiView protein in PROSITE
PS51686 SAM_MT_RSMB_NOP, 1 hit

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

This entry has 4 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
M0R1K5M0R1K5_HUMAN
5-methylcytosine rRNA methyltransfe...
NSUN4
151Annotation score:
Q6ZRQ1Q6ZRQ1_HUMAN
5-methylcytosine rRNA methyltransfe...
NSUN4
652Annotation score:
A0A087WT36A0A087WT36_HUMAN
5-methylcytosine rRNA methyltransfe...
NSUN4
136Annotation score:
A0A087X0V6A0A087X0V6_HUMAN
5-methylcytosine rRNA methyltransfe...
NSUN4
54Annotation score:
A0A087WUV3A0A087WUV3_HUMAN
5-methylcytosine rRNA methyltransfe...
NSUN4
106Annotation score:

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 → A2 PublicationsCorresponds to variant dbSNP:rs3737744Ensembl.1
Natural variantiVAR_032607128N → K. Corresponds to variant dbSNP:rs17102152Ensembl.1
Natural variantiVAR_032608325I → T. Corresponds to variant dbSNP:rs13374337Ensembl.1
Natural variantiVAR_032609365I → V1 PublicationCorresponds to variant dbSNP:rs9865Ensembl.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 No translation available.
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

Similar proteinsi

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 No translation available.
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, 15 interactors
MINTiQ96CB9
STRINGi9606.ENSP00000419740

PTM databases

iPTMnetiQ96CB9
PhosphoSitePlusiQ96CB9

Polymorphism and mutation databases

BioMutaiNSUN4
DMDMi152125805

Proteomic databases

EPDiQ96CB9
MaxQBiQ96CB9
PaxDbiQ96CB9
PeptideAtlasiQ96CB9
PRIDEiQ96CB9
ProteomicsDBi76175
76176 [Q96CB9-2]
76177 [Q96CB9-3]

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
EuPathDBiHostDB:ENSG00000117481.10
GeneCardsiNSUN4
HGNCiHGNC:31802 NSUN4
HPAiHPA028489
MIMi615394 gene
neXtProtiNX_Q96CB9
OpenTargetsiENSG00000117481
PharmGKBiPA134953046
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2198 Eukaryota
COG0144 LUCA
GeneTreeiENSGT00660000095341
HOGENOMiHOG000017426
HOVERGENiHBG106892
InParanoidiQ96CB9
KOiK21970
PhylomeDBiQ96CB9
TreeFamiTF321304

Enzyme and pathway databases

ReactomeiR-HSA-6793080 rRNA modification in the mitochondrion

Miscellaneous databases

ChiTaRSiNSUN4 human
GenomeRNAii387338
PROiPR:Q96CB9
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000117481 Expressed in 199 organ(s), highest expression level in testis
CleanExiHS_NSUN4
ExpressionAtlasiQ96CB9 baseline and differential
GenevisibleiQ96CB9 HS

Family and domain databases

InterProiView protein in InterPro
IPR001678 MeTrfase_RsmB/NOP2
IPR023267 RCMT
IPR029063 SAM-dependent_MTases
PfamiView protein in Pfam
PF01189 Methyltr_RsmB-F, 1 hit
PRINTSiPR02008 RCMTFAMILY
SUPFAMiSSF53335 SSF53335, 1 hit
PROSITEiView protein in PROSITE
PS51686 SAM_MT_RSMB_NOP, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiNSUN4_HUMAN
AccessioniPrimary (citable) accession number: Q96CB9
Secondary accession number(s): A8K6S6
, B3KQ50, B4DHA4, Q5TDF7, Q96AN8, Q9HAJ8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 29, 2007
Last sequence update: May 29, 2007
Last modified: September 12, 2018
This is version 122 of the entry and version 2 of the sequence. See 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, 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. SIMILARITY comments
    Index of protein domains and families
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  6. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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