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Protein

ATP-dependent RNA helicase SUPV3L1, mitochondrial

Gene

SUPV3L1

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

Functioni

Major helicase player in mitochondrial RNA metabolism. Component of the mitochondrial degradosome (mtEXO) complex, that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. ATPase and ATP-dependent multisubstrate helicase, able to unwind double-stranded (ds) DNA and RNA, and RNA/DNA heteroduplexes in the 5'-to-3' direction. Plays a role in the RNA surveillance system in mitochondria; regulates the stability of mature mRNAs, the removal of aberrantly formed mRNAs and the rapid degradation of non coding processing intermediates. Also implicated in recombination and chromatin maintenance pathways. May protect cells from apoptosis. Associates with mitochondrial DNA.7 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Cofactori

Mg2+1 Publication, Mn2+1 Publication

Enzyme regulationi

Helicase activity toward DNA substrate is inhibited by micromolar concentrations of 5,6-dichloro-1-(beta-D-ribofuranosyl)benzotriazole (DRBT) and 4,5,6,7-tetrabromobenzotriazole (TBBT). Helicase activity toward RNA substrate is inhibited by elevated concentrations of TBBT. Inhibited by some ring-expanded nucleoside analogs.2 Publications

Kineticsi

  1. KM=41.9 µM for ATP2 Publications

    pH dependencei

    Optimum pH is 5.0.2 Publications

    Temperature dependencei

    Optimum temperature is 30 degrees Celsius.2 Publications

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi207 – 214ATP8

    GO - Molecular functioni

    • 3'-5' RNA helicase activity Source: UniProtKB
    • ATP binding Source: UniProtKB-KW
    • ATP-dependent RNA helicase activity Source: UniProtKB
    • DNA binding Source: UniProtKB
    • DNA helicase activity Source: UniProtKB
    • double-stranded RNA binding Source: UniProtKB
    • helicase activity Source: ProtInc
    • poly(A) RNA binding Source: UniProtKB
    • protein homodimerization activity Source: UniProtKB
    • RNA binding Source: ProtInc

    GO - Biological processi

    • chromatin maintenance Source: UniProtKB
    • DNA duplex unwinding Source: UniProtKB
    • DNA recombination Source: UniProtKB
    • mitochondrial mRNA catabolic process Source: UniProtKB
    • mitochondrial mRNA surveillance Source: UniProtKB
    • mitochondrial ncRNA surveillance Source: UniProtKB
    • mitochondrial RNA 3'-end processing Source: UniProtKB
    • mitochondrial RNA surveillance Source: UniProtKB
    • mitochondrion morphogenesis Source: UniProtKB
    • negative regulation of apoptotic process Source: UniProtKB
    • positive regulation of cell growth Source: UniProtKB
    • positive regulation of mitochondrial RNA catabolic process Source: UniProtKB
    • RNA catabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Helicase, Hydrolase

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    ATP-dependent RNA helicase SUPV3L1, mitochondrial (EC:3.6.4.13)
    Alternative name(s):
    Suppressor of var1 3-like protein 1
    Short name:
    SUV3-like protein 1
    Gene namesi
    Name:SUPV3L1
    Synonyms:SUV3
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome 10

    Organism-specific databases

    HGNCiHGNC:11471. SUPV3L1.

    Subcellular locationi

    GO - Cellular componenti

    • mitochondrial degradosome Source: UniProtKB
    • mitochondrial matrix Source: UniProtKB
    • mitochondrial nucleoid Source: BHF-UCL
    • mitochondrion Source: UniProtKB
    • nucleus Source: UniProtKB
    Complete GO annotation...

    Keywords - Cellular componenti

    Mitochondrion, Mitochondrion nucleoid, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi207G → V: Abolishes ATPase and dsDNA and dsRNA helicase activities. 1 Publication1
    Mutagenesisi213K → A or R: Abolishes ATPase activity. Abolishes helicase activity and reduces double-stranded RNA degradation. Does not abolish formation of the mitochondrial RNA-degrading complex. 2 Publications1
    Mutagenesisi576 – 581Missing : Does not abolishe ATPase activity. Shows a loss of double-stranded RNA-binding, helicase and degrading activities. 1 Publication6

    Organism-specific databases

    DisGeNETi6832.
    OpenTargetsiENSG00000156502.
    PharmGKBiPA36257.

    Chemistry databases

    ChEMBLiCHEMBL3642.

    Polymorphism and mutation databases

    BioMutaiSUPV3L1.
    DMDMi74759699.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Transit peptidei1 – 22MitochondrionSequence analysisAdd BLAST22
    ChainiPRO_000031054523 – 786ATP-dependent RNA helicase SUPV3L1, mitochondrialAdd BLAST764

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei99N6-acetyllysineCombined sources1
    Modified residuei220N6-acetyllysineCombined sources1
    Modified residuei725PhosphoserineCombined sources1

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    EPDiQ8IYB8.
    MaxQBiQ8IYB8.
    PaxDbiQ8IYB8.
    PeptideAtlasiQ8IYB8.
    PRIDEiQ8IYB8.

    PTM databases

    iPTMnetiQ8IYB8.
    PhosphoSitePlusiQ8IYB8.

    Expressioni

    Tissue specificityi

    Broadly expressed.1 Publication

    Gene expression databases

    BgeeiENSG00000156502.
    CleanExiHS_SUPV3L1.
    ExpressionAtlasiQ8IYB8. baseline and differential.
    GenevisibleiQ8IYB8. HS.

    Organism-specific databases

    HPAiHPA038380.
    HPA038405.

    Interactioni

    Subunit structurei

    Homodimer; in free form. Component of the mitochondrial degradosome (mtEXO) complex which is a heteropentamer containing 2 copies of SUPV3L1 and 3 copies of PNPT1. Interacts with LAMTOR5/HBXIP, WRN and BLM.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    LZTS2Q9BRK43EBI-2876787,EBI-741037

    GO - Molecular functioni

    • protein homodimerization activity Source: UniProtKB

    Protein-protein interaction databases

    BioGridi112699. 20 interactors.
    IntActiQ8IYB8. 4 interactors.
    MINTiMINT-4923961.
    STRINGi9606.ENSP00000352678.

    Structurei

    Secondary structure

    1786
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi61 – 63Combined sources3
    Helixi90 – 102Combined sources13
    Helixi104 – 112Combined sources9
    Helixi117 – 133Combined sources17
    Helixi139 – 149Combined sources11
    Helixi155 – 158Combined sources4
    Helixi159 – 169Combined sources11
    Helixi171 – 174Combined sources4
    Helixi176 – 182Combined sources7
    Helixi188 – 191Combined sources4
    Helixi193 – 196Combined sources4
    Beta strandi201 – 206Combined sources6
    Beta strandi208 – 212Combined sources5
    Helixi213 – 223Combined sources11
    Beta strandi224 – 233Combined sources10
    Helixi234 – 246Combined sources13
    Beta strandi251 – 254Combined sources4
    Beta strandi263 – 266Combined sources4
    Beta strandi270 – 275Combined sources6
    Helixi276 – 278Combined sources3
    Beta strandi281 – 283Combined sources3
    Beta strandi285 – 290Combined sources6
    Helixi293 – 297Combined sources5
    Turni299 – 301Combined sources3
    Helixi302 – 311Combined sources10
    Beta strandi314 – 321Combined sources8
    Helixi323 – 325Combined sources3
    Helixi326 – 336Combined sources11
    Beta strandi340 – 344Combined sources5
    Beta strandi351 – 353Combined sources3
    Helixi361 – 363Combined sources3
    Beta strandi368 – 371Combined sources4
    Helixi375 – 387Combined sources13
    Beta strandi393 – 395Combined sources3
    Helixi401 – 412Combined sources12
    Beta strandi420 – 423Combined sources4
    Helixi425 – 428Combined sources4
    Beta strandi435 – 441Combined sources7
    Helixi461 – 468Combined sources8
    Turni475 – 477Combined sources3
    Beta strandi479 – 487Combined sources9
    Helixi490 – 499Combined sources10
    Beta strandi508 – 510Combined sources3
    Helixi514 – 523Combined sources10
    Helixi529 – 539Combined sources11
    Beta strandi546 – 548Combined sources3
    Helixi552 – 560Combined sources9
    Turni561 – 563Combined sources3
    Helixi568 – 576Combined sources9
    Helixi584 – 598Combined sources15
    Helixi605 – 611Combined sources7
    Helixi622 – 642Combined sources21
    Turni646 – 648Combined sources3
    Helixi652 – 671Combined sources20
    Helixi673 – 682Combined sources10

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3RC3X-ray2.08A47-722[»]
    3RC8X-ray2.90A47-722[»]
    ProteinModelPortaliQ8IYB8.
    SMRiQ8IYB8.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini194 – 334Helicase ATP-bindingAdd BLAST141
    Domaini353 – 518Helicase C-terminalPROSITE-ProRule annotationAdd BLAST166

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni650 – 786Interaction with LAMTOR5, important for protein stabilityAdd BLAST137

    Sequence similaritiesi

    Belongs to the helicase family.Curated
    Contains 1 helicase ATP-binding domain.Curated
    Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiKOG0953. Eukaryota.
    ENOG410XSEY. LUCA.
    GeneTreeiENSGT00390000003100.
    HOGENOMiHOG000175283.
    HOVERGENiHBG108522.
    InParanoidiQ8IYB8.
    KOiK17675.
    OMAiADMIQHI.
    OrthoDBiEOG091G02NO.
    PhylomeDBiQ8IYB8.
    TreeFamiTF106432.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    InterProiIPR001650. Helicase_C.
    IPR027417. P-loop_NTPase.
    IPR022192. SUV3_C.
    [Graphical view]
    PfamiPF00271. Helicase_C. 1 hit.
    PF12513. SUV3_C. 1 hit.
    [Graphical view]
    SMARTiSM00490. HELICc. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 2 hits.
    PROSITEiPS51194. HELICASE_CTER. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q8IYB8-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSFSRALLWA RLPAGRQAGH RAAICSALRP HFGPFPGVLG QVSVLATASS
    60 70 80 90 100
    SASGGSKIPN TSLFVPLTVK PQGPSADGDV GAELTRPLDK NEVKKVLDKF
    110 120 130 140 150
    YKRKEIQKLG ADYGLDARLF HQAFISFRNY IMQSHSLDVD IHIVLNDICF
    160 170 180 190 200
    GAAHADDLFP FFLRHAKQIF PVLDCKDDLR KISDLRIPPN WYPDARAMQR
    210 220 230 240 250
    KIIFHSGPTN SGKTYHAIQK YFSAKSGVYC GPLKLLAHEI FEKSNAAGVP
    260 270 280 290 300
    CDLVTGEERV TVQPNGKQAS HVSCTVEMCS VTTPYEVAVI DEIQMIRDPA
    310 320 330 340 350
    RGWAWTRALL GLCAEEVHLC GEPAAIDLVM ELMYTTGEEV EVRDYKRLTP
    360 370 380 390 400
    ISVLDHALES LDNLRPGDCI VCFSKNDIYS VSRQIEIRGL ESAVIYGSLP
    410 420 430 440 450
    PGTKLAQAKK FNDPNDPCKI LVATDAIGMG LNLSIRRIIF YSLIKPSINE
    460 470 480 490 500
    KGERELEPIT TSQALQIAGR AGRFSSRFKE GEVTTMNHED LSLLKEILKR
    510 520 530 540 550
    PVDPIRAAGL HPTAEQIEMF AYHLPDATLS NLIDIFVDFS QVDGQYFVCN
    560 570 580 590 600
    MDDFKFSAEL IQHIPLSLRV RYVFCTAPIN KKQPFVCSSL LQFARQYSRN
    610 620 630 640 650
    EPLTFAWLRR YIKWPLLPPK NIKDLMDLEA VHDVLDLYLW LSYRFMDMFP
    660 670 680 690 700
    DASLIRDLQK ELDGIIQDGV HNITKLIKMS ETHKLLNLEG FPSGSQSRLS
    710 720 730 740 750
    GTLKSQARRT RGTKALGSKA TEPPSPDAGE LSLASRLVQQ GLLTPDMLKQ
    760 770 780
    LEKEWMTQQT EHNKEKTESG THPKGTRRKK KEPDSD
    Length:786
    Mass (Da):87,991
    Last modified:March 1, 2003 - v1
    Checksum:iFD3BC8EC64C23E42
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti234 – 235KL → TS in AAB97370 (PubMed:10453991).Curated2
    Sequence conflicti254V → E in AAB97370 (PubMed:10453991).Curated1

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_0612142S → F.Corresponds to variant rs33998366dbSNPEnsembl.1
    Natural variantiVAR_03707630P → T.Corresponds to variant rs34596380dbSNPEnsembl.1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF042169 mRNA. Translation: AAB97370.1.
    AK290416 mRNA. Translation: BAF83105.1.
    AL596223 Genomic DNA. Translation: CAH71499.1.
    CH471083 Genomic DNA. Translation: EAW54314.1.
    BC036112 mRNA. Translation: AAH36112.1.
    CCDSiCCDS7287.1.
    RefSeqiNP_001288612.1. NM_001301683.1.
    NP_003162.2. NM_003171.4.
    UniGeneiHs.106469.

    Genome annotation databases

    EnsembliENST00000359655; ENSP00000352678; ENSG00000156502.
    GeneIDi6832.
    KEGGihsa:6832.
    UCSCiuc001jpe.2. human.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF042169 mRNA. Translation: AAB97370.1.
    AK290416 mRNA. Translation: BAF83105.1.
    AL596223 Genomic DNA. Translation: CAH71499.1.
    CH471083 Genomic DNA. Translation: EAW54314.1.
    BC036112 mRNA. Translation: AAH36112.1.
    CCDSiCCDS7287.1.
    RefSeqiNP_001288612.1. NM_001301683.1.
    NP_003162.2. NM_003171.4.
    UniGeneiHs.106469.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3RC3X-ray2.08A47-722[»]
    3RC8X-ray2.90A47-722[»]
    ProteinModelPortaliQ8IYB8.
    SMRiQ8IYB8.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi112699. 20 interactors.
    IntActiQ8IYB8. 4 interactors.
    MINTiMINT-4923961.
    STRINGi9606.ENSP00000352678.

    Chemistry databases

    ChEMBLiCHEMBL3642.

    PTM databases

    iPTMnetiQ8IYB8.
    PhosphoSitePlusiQ8IYB8.

    Polymorphism and mutation databases

    BioMutaiSUPV3L1.
    DMDMi74759699.

    Proteomic databases

    EPDiQ8IYB8.
    MaxQBiQ8IYB8.
    PaxDbiQ8IYB8.
    PeptideAtlasiQ8IYB8.
    PRIDEiQ8IYB8.

    Protocols and materials databases

    DNASUi6832.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000359655; ENSP00000352678; ENSG00000156502.
    GeneIDi6832.
    KEGGihsa:6832.
    UCSCiuc001jpe.2. human.

    Organism-specific databases

    CTDi6832.
    DisGeNETi6832.
    GeneCardsiSUPV3L1.
    HGNCiHGNC:11471. SUPV3L1.
    HPAiHPA038380.
    HPA038405.
    MIMi605122. gene.
    neXtProtiNX_Q8IYB8.
    OpenTargetsiENSG00000156502.
    PharmGKBiPA36257.
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiKOG0953. Eukaryota.
    ENOG410XSEY. LUCA.
    GeneTreeiENSGT00390000003100.
    HOGENOMiHOG000175283.
    HOVERGENiHBG108522.
    InParanoidiQ8IYB8.
    KOiK17675.
    OMAiADMIQHI.
    OrthoDBiEOG091G02NO.
    PhylomeDBiQ8IYB8.
    TreeFamiTF106432.

    Miscellaneous databases

    ChiTaRSiSUPV3L1. human.
    GeneWikiiSUPV3L1.
    GenomeRNAii6832.
    PROiQ8IYB8.
    SOURCEiSearch...

    Gene expression databases

    BgeeiENSG00000156502.
    CleanExiHS_SUPV3L1.
    ExpressionAtlasiQ8IYB8. baseline and differential.
    GenevisibleiQ8IYB8. HS.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    InterProiIPR001650. Helicase_C.
    IPR027417. P-loop_NTPase.
    IPR022192. SUV3_C.
    [Graphical view]
    PfamiPF00271. Helicase_C. 1 hit.
    PF12513. SUV3_C. 1 hit.
    [Graphical view]
    SMARTiSM00490. HELICc. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 2 hits.
    PROSITEiPS51194. HELICASE_CTER. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiSUV3_HUMAN
    AccessioniPrimary (citable) accession number: Q8IYB8
    Secondary accession number(s): A8K301, O43630
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 13, 2007
    Last sequence update: March 1, 2003
    Last modified: November 2, 2016
    This is version 136 of the entry and version 1 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, Reference proteome

    Documents

    1. Human chromosome 10
      Human chromosome 10: 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.