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Protein

Poly(A) RNA polymerase, mitochondrial

Gene

MTPAP

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

Functioni

Polymerase that creates the 3' poly(A) tail of mitochondrial transcripts. Can use all four nucleotides, but has higher activity with ATP and UTP (in vitro). Plays a role in replication-dependent histone mRNA degradation. May be involved in the terminal uridylation of mature histone mRNAs before their degradation is initiated. Might be responsible for the creation of some UAA stop codons which are not encoded in mtDNA.5 Publications

Catalytic activityi

ATP + RNA(n) = diphosphate + RNA(n+1).2 Publications

Cofactori

Mg2+1 Publication, Mn2+1 Publication

Kineticsi

  1. KM=0.1 mM for ATP1 Publication
  2. KM=0.7 mM for UTP1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi243Magnesium or manganese; catalyticBy similarity1
    Metal bindingi245Magnesium or manganese; catalyticBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi107 – 109ATPSequence analysis3
    Nucleotide bindingi241 – 242ATPSequence analysis2

    GO - Molecular functioni

    • ATP binding Source: UniProtKB
    • identical protein binding Source: IntAct
    • magnesium ion binding Source: UniProtKB
    • manganese ion binding Source: UniProtKB
    • poly(A) RNA binding Source: UniProtKB
    • polynucleotide adenylyltransferase activity Source: UniProtKB
    • protein homodimerization activity Source: UniProtKB
    • UTP binding Source: UniProtKB

    GO - Biological processi

    • histone mRNA catabolic process Source: UniProtKB
    • mRNA polyadenylation Source: UniProtKB
    • transcription, DNA-templated Source: UniProtKB-KW
    Complete GO annotation...

    Keywords - Molecular functioni

    Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    mRNA processing, Transcription

    Keywords - Ligandi

    ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding, RNA-binding

    Enzyme and pathway databases

    BioCyciZFISH:HS03048-MONOMER.
    BRENDAi2.7.7.19. 2681.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Poly(A) RNA polymerase, mitochondrial (EC:2.7.7.192 Publications)
    Short name:
    PAP
    Alternative name(s):
    PAP-associated domain-containing protein 1
    Polynucleotide adenylyltransferase
    Terminal uridylyltransferase 1
    Short name:
    TUTase 1
    mtPAP
    Gene namesi
    Name:MTPAP
    Synonyms:PAPD1
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome 10

    Organism-specific databases

    HGNCiHGNC:25532. MTPAP.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm, Mitochondrion

    Pathology & Biotechi

    Involvement in diseasei

    Spastic ataxia 4, autosomal recessive (SPAX4)1 Publication
    The disease is caused by mutations affecting the gene represented in this entry. MTPAP mutations result in a defect of mitochondrial mRNA maturation. Affected individuals exhibit a drastic decrease in poly(A) tail length of mitochondrial mRNA transcripts, including COX1 and RNA14 (PubMed:20970105).1 Publication
    Disease descriptionA slowly progressive neurodegenerative disease characterized by cerebellar ataxia, spastic paraparesis, dysarthria, and optic atrophy.
    See also OMIM:613672
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_064907478N → D in SPAX4. 1 PublicationCorresponds to variant rs267606900dbSNPEnsembl.1

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi221 – 222YF → AA: Reduces dimerization. 1 Publication2
    Mutagenesisi230F → A: Reduced enzyme activity. 1 Publication1
    Mutagenesisi259 – 261HKI → AAA: No effect on dimerization. Loss of dimerization and of enzyme activity; when associated with 294-AAAA-297. 1 Publication3
    Mutagenesisi294 – 297HFGP → AAGA: Reduced dimerization. Loss of dimerization and of enzyme activity; when associated with 259-AAA-261. 1 Publication4
    Mutagenesisi312L → A: Reduced enzyme activity. 1 Publication1
    Mutagenesisi325D → A: Loss of enzyme activity. 1 Publication1
    Mutagenesisi378F → A: Reduced enzyme activity. 1 Publication1

    Keywords - Diseasei

    Disease mutation, Neurodegeneration

    Organism-specific databases

    DisGeNETi55149.
    MalaCardsiMTPAP.
    MIMi613672. phenotype.
    OpenTargetsiENSG00000107951.
    Orphaneti254343. Autosomal recessive spastic ataxia - optic atrophy - dysarthria.
    PharmGKBiPA164723192.

    Polymorphism and mutation databases

    BioMutaiMTPAP.
    DMDMi74753002.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Transit peptidei1 – 37MitochondrionSequence analysisAdd BLAST37
    ChainiPRO_000025068938 – 582Poly(A) RNA polymerase, mitochondrialAdd BLAST545

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei90N6-acetyllysineCombined sources1

    Keywords - PTMi

    Acetylation

    Proteomic databases

    EPDiQ9NVV4.
    MaxQBiQ9NVV4.
    PaxDbiQ9NVV4.
    PeptideAtlasiQ9NVV4.
    PRIDEiQ9NVV4.

    PTM databases

    iPTMnetiQ9NVV4.
    PhosphoSitePlusiQ9NVV4.
    SwissPalmiQ9NVV4.

    Expressioni

    Tissue specificityi

    Ubiquitous, with stronger expression in tissues with high energy requirements: heart, brain, and skeletal muscle.1 Publication

    Gene expression databases

    BgeeiENSG00000107951.
    ExpressionAtlasiQ9NVV4. baseline and differential.
    GenevisibleiQ9NVV4. HS.

    Organism-specific databases

    HPAiHPA038620.
    HPA058232.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself3EBI-2556166,EBI-2556166
    Azi2Q9QYP62EBI-2556166,EBI-6115874From a different organism.
    CALCOCO2Q131372EBI-2556166,EBI-739580
    TBK1Q9UHD22EBI-2556166,EBI-356402

    GO - Molecular functioni

    • identical protein binding Source: IntAct
    • protein homodimerization activity Source: UniProtKB

    Protein-protein interaction databases

    BioGridi120452. 23 interactors.
    IntActiQ9NVV4. 13 interactors.
    MINTiMINT-4831364.
    STRINGi9606.ENSP00000263063.

    Structurei

    Secondary structure

    1582
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi64 – 75Combined sources12
    Beta strandi77 – 82Combined sources6
    Helixi90 – 95Combined sources6
    Helixi96 – 98Combined sources3
    Beta strandi104 – 107Combined sources4
    Beta strandi109 – 117Combined sources9
    Helixi125 – 128Combined sources4
    Helixi174 – 180Combined sources7
    Beta strandi183 – 185Combined sources3
    Helixi186 – 197Combined sources12
    Helixi201 – 218Combined sources18
    Turni219 – 221Combined sources3
    Beta strandi226 – 230Combined sources5
    Helixi231 – 233Combined sources3
    Beta strandi244 – 249Combined sources6
    Helixi277 – 294Combined sources18
    Beta strandi299 – 305Combined sources7
    Beta strandi307 – 310Combined sources4
    Beta strandi312 – 317Combined sources6
    Turni318 – 320Combined sources3
    Beta strandi323 – 327Combined sources5
    Helixi333 – 344Combined sources12
    Helixi348 – 363Combined sources16
    Helixi377 – 389Combined sources13
    Helixi403 – 406Combined sources4
    Helixi437 – 447Combined sources11
    Helixi448 – 450Combined sources3
    Helixi492 – 510Combined sources19
    Helixi528 – 530Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3PQ1X-ray3.10A/B44-134[»]
    A/B172-452[»]
    A/B490-538[»]
    ProteinModelPortaliQ9NVV4.
    SMRiQ9NVV4.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9NVV4.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini437 – 483PAP-associatedAdd BLAST47

    Sequence similaritiesi

    Belongs to the DNA polymerase type-B-like family.Curated
    Contains 1 PAP-associated domain.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiKOG2277. Eukaryota.
    COG5260. LUCA.
    GeneTreeiENSGT00550000074490.
    HOGENOMiHOG000115438.
    HOVERGENiHBG082104.
    InParanoidiQ9NVV4.
    KOiK18060.
    OMAiTHKTSGN.
    OrthoDBiEOG091G091J.
    PhylomeDBiQ9NVV4.
    TreeFamiTF354308.

    Family and domain databases

    InterProiIPR002058. PAP_assoc.
    [Graphical view]
    PfamiPF03828. PAP_assoc. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

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

    This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

    Isoform 1 (identifier: Q9NVV4-1) [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
    MAVPGVGLLT RLNLCARRRT RVQRPIVRLL SCPGTVAKDL RRDEQPSGSV
    60 70 80 90 100
    ETGFEDKIPK RRFSEMQNER REQAQRTVLI HCPEKISENK FLKYLSQFGP
    110 120 130 140 150
    INNHFFYESF GLYAVVEFCQ KESIGSLQNG THTPSTAMET AIPFRSRFFN
    160 170 180 190 200
    LKLKNQTSER SRVRSSNQLP RSNKQLFELL CYAESIDDQL NTLLKEFQLT
    210 220 230 240 250
    EENTKLRYLT CSLIEDMAAA YFPDCIVRPF GSSVNTFGKL GCDLDMFLDL
    260 270 280 290 300
    DETRNLSAHK ISGNFLMEFQ VKNVPSERIA TQKILSVLGE CLDHFGPGCV
    310 320 330 340 350
    GVQKILNARC PLVRFSHQAS GFQCDLTTNN RIALTSSELL YIYGALDSRV
    360 370 380 390 400
    RALVFSVRCW ARAHSLTSSI PGAWITNFSL TMMVIFFLQR RSPPILPTLD
    410 420 430 440 450
    SLKTLADAED KCVIEGNNCT FVRDLSRIKP SQNTETLELL LKEFFEYFGN
    460 470 480 490 500
    FAFDKNSINI RQGREQNKPD SSPLYIQNPF ETSLNISKNV SQSQLQKFVD
    510 520 530 540 550
    LARESAWILQ QEDTDRPSIS SNRPWGLVSL LLPSAPNRKS FTKKKSNKFA
    560 570 580
    IETVKNLLES LKGNRTENFT KTSGKRTIST QT
    Length:582
    Mass (Da):66,172
    Last modified:October 1, 2000 - v1
    Checksum:iEBA5BECEA39A5090
    GO
    Isoform 2 (identifier: Q9NVV4-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-52: MAVPGVGLLT...DEQPSGSVET → MAWAKKVGGR...QELGAADKQG

    Note: No experimental confirmation available.
    Show »
    Length:712
    Mass (Da):78,833
    Checksum:i90B570568F0B7A26
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti507W → L in BAB13981 (PubMed:14702039).Curated1
    Sequence conflicti554V → A in BAB13981 (PubMed:14702039).Curated1

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_027601162R → C.Corresponds to variant rs1047991dbSNPEnsembl.1
    Natural variantiVAR_027602221Y → H.1 PublicationCorresponds to variant rs17855118dbSNPEnsembl.1
    Natural variantiVAR_027603419C → R.1 PublicationCorresponds to variant rs17857517dbSNPEnsembl.1
    Natural variantiVAR_064907478N → D in SPAX4. 1 PublicationCorresponds to variant rs267606900dbSNPEnsembl.1
    Natural variantiVAR_027604546S → N.1 PublicationCorresponds to variant rs17855116dbSNPEnsembl.1

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_0207241 – 52MAVPG…GSVET → MAWAKKVGGRAGQGRSLSRC DPIILDPEWLYGPPEGEGGP EGVGGETRASIHPPLRTGRH HQKVNHNIRGPEGSAKDAAP GGGGHHQAGPGQRGDEDGAL QHLCGGGGGVGVSVGRGTGT SVAAEHPSLQVKLLELQELV LRLAGDHNEGHGKFLAAAQN PADDPAPGAPAPQELGAADK QG in isoform 2. 1 PublicationAdd BLAST52

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB194709 mRNA. Translation: BAD98252.1.
    AY364242 mRNA. Translation: AAQ76801.1.
    AK001348 mRNA. Translation: BAA91641.1.
    AK022188 mRNA. Translation: BAB13981.1.
    AL122121 mRNA. Translation: CAH56395.1.
    AL353796, AL161651 Genomic DNA. Translation: CAH72262.1.
    AL161651, AL353796 Genomic DNA. Translation: CAI14218.1.
    CH471072 Genomic DNA. Translation: EAW86014.1.
    CH471072 Genomic DNA. Translation: EAW86015.1.
    BC061703 mRNA. Translation: AAH61703.1.
    CCDSiCCDS7165.1. [Q9NVV4-1]
    RefSeqiNP_060579.3. NM_018109.3. [Q9NVV4-1]
    UniGeneiHs.173946.

    Genome annotation databases

    EnsembliENST00000263063; ENSP00000263063; ENSG00000107951. [Q9NVV4-1]
    GeneIDi55149.
    KEGGihsa:55149.
    UCSCiuc001iva.5. human. [Q9NVV4-1]

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB194709 mRNA. Translation: BAD98252.1.
    AY364242 mRNA. Translation: AAQ76801.1.
    AK001348 mRNA. Translation: BAA91641.1.
    AK022188 mRNA. Translation: BAB13981.1.
    AL122121 mRNA. Translation: CAH56395.1.
    AL353796, AL161651 Genomic DNA. Translation: CAH72262.1.
    AL161651, AL353796 Genomic DNA. Translation: CAI14218.1.
    CH471072 Genomic DNA. Translation: EAW86014.1.
    CH471072 Genomic DNA. Translation: EAW86015.1.
    BC061703 mRNA. Translation: AAH61703.1.
    CCDSiCCDS7165.1. [Q9NVV4-1]
    RefSeqiNP_060579.3. NM_018109.3. [Q9NVV4-1]
    UniGeneiHs.173946.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3PQ1X-ray3.10A/B44-134[»]
    A/B172-452[»]
    A/B490-538[»]
    ProteinModelPortaliQ9NVV4.
    SMRiQ9NVV4.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi120452. 23 interactors.
    IntActiQ9NVV4. 13 interactors.
    MINTiMINT-4831364.
    STRINGi9606.ENSP00000263063.

    PTM databases

    iPTMnetiQ9NVV4.
    PhosphoSitePlusiQ9NVV4.
    SwissPalmiQ9NVV4.

    Polymorphism and mutation databases

    BioMutaiMTPAP.
    DMDMi74753002.

    Proteomic databases

    EPDiQ9NVV4.
    MaxQBiQ9NVV4.
    PaxDbiQ9NVV4.
    PeptideAtlasiQ9NVV4.
    PRIDEiQ9NVV4.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000263063; ENSP00000263063; ENSG00000107951. [Q9NVV4-1]
    GeneIDi55149.
    KEGGihsa:55149.
    UCSCiuc001iva.5. human. [Q9NVV4-1]

    Organism-specific databases

    CTDi55149.
    DisGeNETi55149.
    GeneCardsiMTPAP.
    HGNCiHGNC:25532. MTPAP.
    HPAiHPA038620.
    HPA058232.
    MalaCardsiMTPAP.
    MIMi613669. gene.
    613672. phenotype.
    neXtProtiNX_Q9NVV4.
    OpenTargetsiENSG00000107951.
    Orphaneti254343. Autosomal recessive spastic ataxia - optic atrophy - dysarthria.
    PharmGKBiPA164723192.
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiKOG2277. Eukaryota.
    COG5260. LUCA.
    GeneTreeiENSGT00550000074490.
    HOGENOMiHOG000115438.
    HOVERGENiHBG082104.
    InParanoidiQ9NVV4.
    KOiK18060.
    OMAiTHKTSGN.
    OrthoDBiEOG091G091J.
    PhylomeDBiQ9NVV4.
    TreeFamiTF354308.

    Enzyme and pathway databases

    BioCyciZFISH:HS03048-MONOMER.
    BRENDAi2.7.7.19. 2681.

    Miscellaneous databases

    ChiTaRSiMTPAP. human.
    EvolutionaryTraceiQ9NVV4.
    GenomeRNAii55149.
    PROiQ9NVV4.
    SOURCEiSearch...

    Gene expression databases

    BgeeiENSG00000107951.
    ExpressionAtlasiQ9NVV4. baseline and differential.
    GenevisibleiQ9NVV4. HS.

    Family and domain databases

    InterProiIPR002058. PAP_assoc.
    [Graphical view]
    PfamiPF03828. PAP_assoc. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPAPD1_HUMAN
    AccessioniPrimary (citable) accession number: Q9NVV4
    Secondary accession number(s): D3DRX0
    , Q659E3, Q6P7E5, Q9HA74
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 3, 2006
    Last sequence update: October 1, 2000
    Last modified: November 30, 2016
    This is version 131 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.