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Q96CB9 (NSUN4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 84. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
5-methylcytosine rRNA methyltransferase NSUN4

EC=2.1.1.-
Alternative name(s):
NOL1/NOP2/Sun domain family member 4
Gene names
Name:NSUN4
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length384 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

5-methylcytosine rRNA methyltransferase involved in mitochondrial ribosome large subunit biogenesis. Ref.5

Subunit structure

Heterodimer with MTERFD2/MTERF4; this interaction may be required for NSUN4 recruitment to the mitochondrial large ribosomal subunit.

Subcellular location

Mitochondrion Ref.5 Ref.8 Ref.9.

Sequence similarities

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

Ontologies

Keywords
   Biological processrRNA processing
   Cellular componentMitochondrion
   Coding sequence diversityAlternative splicing
Polymorphism
   DomainTransit peptide
   LigandRNA-binding
S-adenosyl-L-methionine
   Molecular functionMethyltransferase
Transferase
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processrRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentmitochondrial large ribosomal subunit

Inferred from direct assay Ref.5. Source: MGI

   Molecular_functionRNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

methyltransferase activity

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q96CB9-1)

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.
Isoform 2 (identifier: Q96CB9-2)

The sequence of this isoform differs from the canonical sequence as follows:
     147-384: Missing.
Note: No experimental confirmation available.
Isoform 3 (identifier: Q96CB9-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-198: Missing.
     199-219: NLAANDLSPSRIARLQKILHS → MLPPCCLFWPSACSLGTSCLT
Note: No experimental confirmation available.
Isoform 4 (identifier: Q96CB9-4)

The sequence of this isoform differs from the canonical sequence as follows:
     1-49: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 2525Mitochondrion
Chain26 – 3843595-methylcytosine rRNA methyltransferase NSUN4
PRO_0000289234

Regions

Region181 – 1877S-adenosyl-L-methionine binding

Sites

Active site3101Nucleophile Ref.8
Binding site2371S-adenosyl-L-methionine
Binding site2551S-adenosyl-L-methionine

Natural variations

Alternative sequence1 – 198198Missing in isoform 3.
VSP_025971
Alternative sequence1 – 4949Missing in isoform 4.
VSP_045053
Alternative sequence147 – 384238Missing in isoform 2.
VSP_025972
Alternative sequence199 – 21921NLAAN…KILHS → MLPPCCLFWPSACSLGTSCL T in isoform 3.
VSP_025973
Natural variant511T → A. Ref.1 Ref.4
Corresponds to variant rs3737744 [ dbSNP | Ensembl ].
VAR_032606
Natural variant1281N → K.
Corresponds to variant rs17102152 [ dbSNP | Ensembl ].
VAR_032607
Natural variant3251I → T.
Corresponds to variant rs13374337 [ dbSNP | Ensembl ].
VAR_032608
Natural variant3651I → V. Ref.1
Corresponds to variant rs9865 [ dbSNP | Ensembl ].
VAR_032609

Experimental info

Sequence conflict2821Q → R in BAG51912. Ref.1

Secondary structure

............................................................ 384
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 29, 2007. Version 2.
Checksum: 4D83B6D55D65C27F

FASTA38443,089
        10         20         30         40         50         60 
MAALTLRGVR ELLKRVDLAT VPRRHRYKKK WAATEPKFPA VRLALQNFDM TYSVQFGDLW 

        70         80         90        100        110        120 
PSIRVSLLSE QKYGALVNNF AAWDHVSAKL EQLSAKDFVN EAISHWELQS EGGQSAAPSP 

       130        140        150        160        170        180 
ASWACSPNLR CFTFDRGDIS RFPPARPGSL GVMEYYLMDA ASLLPVLALG LQPGDIVLDL 

       190        200        210        220        230        240 
CAAPGGKTLA LLQTGCCRNL AANDLSPSRI ARLQKILHSY VPEEIRDGNQ VRVTSWDGRK 

       250        260        270        280        290        300 
WGELEGDTYD RVLVDVPCTT DRHSLHEEEN NIFKRSRKKE RQILPVLQVQ LLAAGLLATK 

       310        320        330        340        350        360 
PGGHVVYSTC SLSHLQNEYV VQGAIELLAN QYSIQVQVED LTHFRRVFMD TFCFFSSCQV 

       370        380 
GELVIPNLMA NFGPMYFCKM RRLT 

« Hide

Isoform 2 [UniParc].

Checksum: E49A839AA5937FB5
Show »

FASTA14616,507
Isoform 3 [UniParc].

Checksum: 4186007A46B086CD
Show »

FASTA18621,240
Isoform 4 [UniParc].

Checksum: 85AACD29E9DDB7D7
Show »

FASTA33537,374

References

« Hide 'large scale' references
[1]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 3 AND 4), VARIANTS ALA-51 AND VAL-365.
Tissue: Brain, Embryo, Placenta and Testis.
[2]"The DNA sequence and biological annotation of human chromosome 1."
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. expand/collapse author list , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 96-384 (ISOFORM 2), VARIANT ALA-51.
Tissue: Colon and Duodenum.
[5]"MTERF4 regulates translation by targeting the methyltransferase NSUN4 to the mammalian mitochondrial ribosome."
Camara Y., Asin-Cayuela J., Park C.B., Metodiev M.D., Shi Y., Ruzzenente B., Kukat C., Habermann B., Wibom R., Hultenby K., Franz T., Erdjument-Bromage H., Tempst P., Hallberg B.M., Gustafsson C.M., Larsson N.G.
Cell Metab. 13:527-539(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PARTIAL PROTEIN SEQUENCE, TRANSIT PEPTIDE CLEAVAGE SITE, FUNCTION, INTERACTION WITH MTERFD2, SUBCELLULAR LOCATION.
[6]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[7]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]"Structure of the human MTERF4-NSUN4 protein complex that regulates mitochondrial ribosome biogenesis."
Spahr H., Habermann B., Gustafsson C.M., Larsson N.G., Hallberg B.M.
Proc. Natl. Acad. Sci. U.S.A. 109:15253-15258(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 26-384 IN COMPLEX WITH MTERF4, ACTIVE SITE, SUBCELLULAR LOCATION.
[9]"Structure of the essential MTERF4:NSUN4 protein complex reveals how an MTERF protein collaborates to facilitate rRNA modification."
Yakubovskaya E., Guja K.E., Mejia E., Castano S., Hambardjieva E., Choi W.S., Garcia-Diaz M.
Structure 20:1940-1947(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 26-384 IN COMPLEX WITH S-ADENOSYL-L-METHIONINE AND MTERF4, SUBCELLULAR LOCATION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_001243056.1. NM_001256127.1.
NP_001243057.1. NM_001256128.1.
NP_950245.2. NM_199044.3.
UniGeneHs.163424.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4FP9X-ray2.90A/C/D/F26-384[»]
4FZVX-ray2.00A26-384[»]
ProteinModelPortalQ96CB9.
SMRQ96CB9. Positions 38-384.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid132288. 8 interactions.
DIPDIP-58104N.
IntActQ96CB9. 6 interactions.
MINTMINT-1474456.
STRING9606.ENSP00000419740.

PTM databases

PhosphoSiteQ96CB9.

Polymorphism databases

DMDM152125805.

Proteomic databases

PaxDbQ96CB9.
PRIDEQ96CB9.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000474844; ENSP00000419740; ENSG00000117481. [Q96CB9-1]
ENST00000536062; ENSP00000438912; ENSG00000117481. [Q96CB9-4]
ENST00000537428; ENSP00000437758; ENSG00000117481. [Q96CB9-4]
GeneID387338.
KEGGhsa:387338.
UCSCuc001cpr.2. human. [Q96CB9-1]

Organism-specific databases

CTD387338.
GeneCardsGC01P046805.
HGNCHGNC:31802. NSUN4.
HPAHPA027958.
HPA028489.
MIM615394. gene.
neXtProtNX_Q96CB9.
PharmGKBPA134953046.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0144.
HOGENOMHOG000017426.
HOVERGENHBG106892.
InParanoidQ96CB9.
OMAACSPNLR.
OrthoDBEOG789CB3.
PhylomeDBQ96CB9.
TreeFamTF321304.

Gene expression databases

ArrayExpressQ96CB9.
BgeeQ96CB9.
CleanExHS_NSUN4.
GenevestigatorQ96CB9.

Family and domain databases

InterProIPR001678. Fmu/NOL1/Nop2p.
IPR023267. RCMT.
[Graphical view]
PfamPF01189. Nol1_Nop2_Fmu. 1 hit.
[Graphical view]
PRINTSPR02008. RCMTFAMILY.
PROSITEPS51686. SAM_MT_RSMB_NOP. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GenomeRNAi387338.
NextBio101304.
PROQ96CB9.
SOURCESearch...

Entry information

Entry nameNSUN4_HUMAN
AccessionPrimary (citable) accession number: Q96CB9
Secondary accession number(s): A8K6S6 expand/collapse secondary AC list , B3KQ50, B4DHA4, Q5TDF7, Q96AN8, Q9HAJ8
Entry history
Integrated into UniProtKB/Swiss-Prot: May 29, 2007
Last sequence update: May 29, 2007
Last modified: April 16, 2014
This is version 84 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM