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Protein

tRNA (cytosine(34)-C(5))-methyltransferase, mitochondrial

Gene

NSUN3

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

Functioni

Mitochondrial tRNA methyltransferase that mediates methylation of cytosine to 5-methylcytosine (m5C) at position 34 of mt-tRNA(Met) (PubMed:27497299, PubMed:27214402, PubMed:27356879). mt-tRNA(Met) methylation at cytosine(34) takes place at the wobble position of the anticodon and initiates the formation of 5-formylcytosine (f5c) at this position (PubMed:27497299, PubMed:27214402, PubMed:27356879). mt-tRNA(Met) containing the f5c modification at the wobble position enables recognition of the AUA codon in addition to the AUG codon, expanding codon recognition in mitochondrial translation (PubMed:27497299, PubMed:27356879).3 Publications

Catalytic activityi

S-adenosyl-L-methionine + cytosine(34) in mitochondrial tRNA(Met) = S-adenosyl-L-homocysteine + 5-methylcytosine(34) in mitochondrial tRNA(Met).3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei162S-adenosyl-L-methioninePROSITE-ProRule annotation1
Binding sitei193S-adenosyl-L-methioninePROSITE-ProRule annotation1
Binding sitei211S-adenosyl-L-methioninePROSITE-ProRule annotation1
Active sitei265NucleophilePROSITE-ProRule annotation1 Publication1

GO - Molecular functioni

  • methyltransferase activity Source: GO_Central
  • tRNA (cytosine-5-)-methyltransferase activity Source: UniProtKB
  • tRNA binding Source: UniProtKB-KW

GO - Biological processi

  • regulation of mitochondrial translation Source: UniProtKB
  • rRNA methylation Source: GO_Central
  • tRNA wobble base cytosine methylation Source: UniProtKB

Keywordsi

Molecular functionMethyltransferase, RNA-binding, Transferase, tRNA-binding
LigandS-adenosyl-L-methionine

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA (cytosine(34)-C(5))-methyltransferase, mitochondrial (EC:2.1.1.-3 Publications)
Alternative name(s):
NOL1/NOP2/Sun domain family member 3Imported
Gene namesi
Name:NSUN3Imported
ORF Names:MSTP0771 Publication, UG0651E061 Publication
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

EuPathDBiHostDB:ENSG00000178694.9
HGNCiHGNC:26208 NSUN3
MIMi617491 gene
neXtProtiNX_Q9H649

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

Involvement in diseasei

Mitochondrial complex deficiency (PubMed:27356879). A disorder of the mitochondrial respiratory chain resulting in a highly variable phenotype depending on which tissues are affected (PubMed:27356879). Clinical features include combined developmental disability, microcephaly, failure to thrive, recurrent increased lactate levels in plasma, muscular weakness, proximal accentuated, external ophthalmoplegia and convergence nystagmus (PubMed:27356879). Defects are probably caused by deficient methylation and formylation of mt-tRNA(Met) wobble cytosine (PubMed:27356879). The disease may be caused by mutations affecting the gene represented in this entry.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi214C → A in C2A; catalytic mutant. Abolishes ability to methylate mt-tRNA(Met). 1 Publication1
Mutagenesisi265C → A: Catalytic mutant. Abolishes ability to methylate mt-tRNA(Met). 1 Publication1

Keywords - Diseasei

Disease mutation, Primary mitochondrial disease

Organism-specific databases

DisGeNETi63899
OpenTargetsiENSG00000178694
PharmGKBiPA134961151

Polymorphism and mutation databases

BioMutaiNSUN3
DMDMi74733593

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002892301 – 340tRNA (cytosine(34)-C(5))-methyltransferase, mitochondrialAdd BLAST340

Proteomic databases

EPDiQ9H649
MaxQBiQ9H649
PaxDbiQ9H649
PeptideAtlasiQ9H649
PRIDEiQ9H649
ProteomicsDBi80957

PTM databases

iPTMnetiQ9H649
PhosphoSitePlusiQ9H649

Expressioni

Gene expression databases

BgeeiENSG00000178694 Expressed in 172 organ(s), highest expression level in bone marrow
CleanExiHS_NSUN3
ExpressionAtlasiQ9H649 baseline and differential
GenevisibleiQ9H649 HS

Organism-specific databases

HPAiHPA036181
HPA057979

Interactioni

Protein-protein interaction databases

BioGridi121978, 13 interactors
STRINGi9606.ENSP00000318986

Structurei

3D structure databases

ProteinModelPortaliQ9H649
SMRiQ9H649
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni139 – 145S-adenosyl-L-methionine bindingPROSITE-ProRule annotation7

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG2198 Eukaryota
COG0144 LUCA
GeneTreeiENSGT00660000095341
HOGENOMiHOG000017426
HOVERGENiHBG106892
InParanoidiQ9H649
KOiK21969
OMAiMYVAKLK
OrthoDBiEOG091G07PM
PhylomeDBiQ9H649
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

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

Q9H649-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MLTQLKAKSE GKLAKQICKV VLDHFEKQYS KELGDAWNTV REILTSPSCW
60 70 80 90 100
QYAVLLNRFN YPFELEKDLH LKGYHTLSQG SLPNYPKSVK CYLSRTPGRI
110 120 130 140 150
PSERHQIGNL KKYYLLNAAS LLPVLALELR DGEKVLDLCA APGGKSIALL
160 170 180 190 200
QCACPGYLHC NEYDSLRLRW LRQTLESFIP QPLINVIKVS ELDGRKMGDA
210 220 230 240 250
QPEMFDKVLV DAPCSNDRSW LFSSDSQKAS CRISQRRNLP LLQIELLRSA
260 270 280 290 300
IKALRPGGIL VYSTCTLSKA ENQDVISEIL NSHGNIMPMD IKGIARTCSH
310 320 330 340
DFTFAPTGQE CGLLVIPDKG KAWGPMYVAK LKKSWSTGKW
Length:340
Mass (Da):38,244
Last modified:March 1, 2001 - v1
Checksum:i7E09AF2E477EB6F3
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F8WF52F8WF52_HUMAN
tRNA (cytosine(34)-C(5))-methyltran...
NSUN3
77Annotation score:

Sequence cautioni

The sequence AAN76512 differs from that shown. Chimera.Curated
The sequence AAQ13600 differs from that shown. Reason: Frameshift at position 98.Curated
The sequence BAB15234 differs from that shown. Reason: Erroneous initiation.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_07744599 – 340Missing Probable disease-associated mutation found in a patient with disorder of the mitochondrial respiratory chain. 1 PublicationAdd BLAST242
Natural variantiVAR_032605295A → V1 PublicationCorresponds to variant dbSNP:rs17854922Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK025762 mRNA Translation: BAB15234.1 Different initiation.
AK026262 mRNA Translation: BAB15417.1
AF169972 mRNA Translation: AAQ13600.1 Frameshift.
BC020602 mRNA Translation: AAH20602.1
BC057238 mRNA Translation: AAH57238.1
AF351612 mRNA Translation: AAN76512.1 Sequence problems.
CCDSiCCDS2927.1
RefSeqiNP_071355.1, NM_022072.4
UniGeneiHs.436594
Hs.448003

Genome annotation databases

EnsembliENST00000314622; ENSP00000318986; ENSG00000178694
GeneIDi63899
KEGGihsa:63899
UCSCiuc003drl.2 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK025762 mRNA Translation: BAB15234.1 Different initiation.
AK026262 mRNA Translation: BAB15417.1
AF169972 mRNA Translation: AAQ13600.1 Frameshift.
BC020602 mRNA Translation: AAH20602.1
BC057238 mRNA Translation: AAH57238.1
AF351612 mRNA Translation: AAN76512.1 Sequence problems.
CCDSiCCDS2927.1
RefSeqiNP_071355.1, NM_022072.4
UniGeneiHs.436594
Hs.448003

3D structure databases

ProteinModelPortaliQ9H649
SMRiQ9H649
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121978, 13 interactors
STRINGi9606.ENSP00000318986

PTM databases

iPTMnetiQ9H649
PhosphoSitePlusiQ9H649

Polymorphism and mutation databases

BioMutaiNSUN3
DMDMi74733593

Proteomic databases

EPDiQ9H649
MaxQBiQ9H649
PaxDbiQ9H649
PeptideAtlasiQ9H649
PRIDEiQ9H649
ProteomicsDBi80957

Protocols and materials databases

DNASUi63899
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000314622; ENSP00000318986; ENSG00000178694
GeneIDi63899
KEGGihsa:63899
UCSCiuc003drl.2 human

Organism-specific databases

CTDi63899
DisGeNETi63899
EuPathDBiHostDB:ENSG00000178694.9
GeneCardsiNSUN3
HGNCiHGNC:26208 NSUN3
HPAiHPA036181
HPA057979
MIMi617491 gene
neXtProtiNX_Q9H649
OpenTargetsiENSG00000178694
PharmGKBiPA134961151
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2198 Eukaryota
COG0144 LUCA
GeneTreeiENSGT00660000095341
HOGENOMiHOG000017426
HOVERGENiHBG106892
InParanoidiQ9H649
KOiK21969
OMAiMYVAKLK
OrthoDBiEOG091G07PM
PhylomeDBiQ9H649
TreeFamiTF321304

Miscellaneous databases

ChiTaRSiNSUN3 human
GenomeRNAii63899
PROiPR:Q9H649
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000178694 Expressed in 172 organ(s), highest expression level in bone marrow
CleanExiHS_NSUN3
ExpressionAtlasiQ9H649 baseline and differential
GenevisibleiQ9H649 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 nameiNSUN3_HUMAN
AccessioniPrimary (citable) accession number: Q9H649
Secondary accession number(s): Q6PG41, Q8IXG9, Q9H6M2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 29, 2007
Last sequence update: March 1, 2001
Last modified: November 7, 2018
This is version 115 of the entry and version 1 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

Complete proteome, Reference proteome

Documents

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