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Protein

Non-canonical poly(A) RNA polymerase PAPD7

Gene

PAPD7

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

Functioni

Catalytic subunit of a TRAMP-like complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism. Polyadenylation with short oligo(A) tails is required for the degradative activity of the exosome on several of its nuclear RNA substrates. Has no terminal uridylyltransferase activity, and does not play a role in replication-dependent histone mRNA degradation via uridylation.1 Publication

Catalytic activityi

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

Cofactori

Mg2+By similarity, Mn2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi277 – 2771Magnesium or manganese; catalyticBy similarity
Metal bindingi279 – 2791Magnesium or manganese; catalyticBy similarity

GO - Molecular functioni

GO - Biological processi

  • cell division Source: UniProtKB-KW
  • double-strand break repair Source: UniProtKB
  • mitotic chromosome condensation Source: UniProtKB
  • response to drug Source: UniProtKB
  • sister chromatid cohesion Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Nucleotidyltransferase, Transferase

Keywords - Biological processi

Cell cycle, Cell division, Mitosis

Keywords - Ligandi

DNA-binding, Magnesium, Manganese, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Non-canonical poly(A) RNA polymerase PAPD7 (EC:2.7.7.19)
Alternative name(s):
DNA polymerase sigma
LAK-1
PAP-associated domain-containing protein 7
TRAMP-like complex polyadenylate polymerase
Terminal uridylyltransferase 5
Short name:
TUTase 5
Topoisomerase-related function protein 4-1
Short name:
TRF4-1
Gene namesi
Name:PAPD7
Synonyms:POLS, TRF4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:16705. PAPD7.

Subcellular locationi

  • Cytoplasm 1 Publication
  • Nucleusnucleoplasm 1 Publication

  • Note: Excluded from nucleolus, weak staining detected in the cytoplasm.

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nucleoplasm Source: UniProtKB-SubCell
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi167 – 23064Missing : Localizes to cytoplasm. 1 PublicationAdd
BLAST

Organism-specific databases

PharmGKBiPA33523.

Polymorphism and mutation databases

BioMutaiPAPD7.
DMDMi60392922.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 772772Non-canonical poly(A) RNA polymerase PAPD7PRO_0000120308Add
BLAST

Proteomic databases

EPDiQ5XG87.
MaxQBiQ5XG87.
PaxDbiQ5XG87.
PRIDEiQ5XG87.

PTM databases

PhosphoSiteiQ5XG87.

Expressioni

Gene expression databases

BgeeiQ5XG87.
CleanExiHS_POLS.
ExpressionAtlasiQ5XG87. baseline and differential.
GenevisibleiQ5XG87. HS.

Organism-specific databases

HPAiHPA045487.
HPA046742.

Interactioni

Subunit structurei

Component of a nuclear TRAMP-like complex, an ATP-dependent exosome regulatory complex consisting of a helicase (SKIV2L2/MTR4), an oligadenylate polymerase (PAPD5 or PAPD7), and a substrate specific RNA-binding factor (ZCCHC7 or ZCCHC8). Several TRAMP-like complexes exist with specific compositions and are associated with nuclear, or nucleolar RNA exosomes.

GO - Molecular functioni

  • SMC family protein binding Source: UniProtKB

Protein-protein interaction databases

BioGridi116232. 4 interactions.
IntActiQ5XG87. 1 interaction.
MINTiMINT-2999333.
STRINGi9606.ENSP00000230859.

Structurei

3D structure databases

ProteinModelPortaliQ5XG87.
SMRiQ5XG87. Positions 223-516.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini408 – 46861PAP-associatedAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi27 – 7953Ala-richAdd
BLAST
Compositional biasi85 – 11733Ser-richAdd
BLAST
Compositional biasi576 – 60227Ser-richAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG1906. Eukaryota.
COG5260. LUCA.
GeneTreeiENSGT00400000022055.
HOGENOMiHOG000290646.
HOVERGENiHBG053636.
InParanoidiQ5XG87.
KOiK03514.
OMAiHSGMKLS.
OrthoDBiEOG7X6KZP.
TreeFamiTF313939.

Family and domain databases

InterProiIPR002058. PAP_assoc.
IPR002934. Polymerase_NTP_transf_dom.
[Graphical view]
PfamiPF01909. NTP_transf_2. 1 hit.
PF03828. PAP_assoc. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q5XG87-1) [UniParc]FASTAAdd to basket

Also known as: l

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
MQIWETSQGV GRGGSGFASY FCLNSPALDT AAAAGAAGRG SGGLGPALPA
60 70 80 90 100
ASPPPPGPTA PAALPPALLT ALGPAAEGAR RLHKSPSLSS SSSSSSSNAE
110 120 130 140 150
SGTESPGCSS SSSSSASLGR PGGGRGGAFF NFADGAPSAP GTANGHPGPR
160 170 180 190 200
GPAPAGSPSQ HQFHPGRRKR ENKASTYGLN YLLSGSRAAA LSGGGGPGAQ
210 220 230 240 250
APRPGTPWKS RAYSPGIQGL HEEIIDFYNF MSPCPEEAAM RREVVKRIET
260 270 280 290 300
VVKDLWPTAD VQIFGSFSTG LYLPTSDIDL VVFGKWERPP LQLLEQALRK
310 320 330 340 350
HNVAEPCSIK VLDKATVPII KLTDQETEVK VDISFNMETG VRAAEFIKNY
360 370 380 390 400
MKKYSLLPYL ILVLKQFLLQ RDLNEVFTGG ISSYSLILMA ISFLQLHPRI
410 420 430 440 450
DARRADENLG MLLVEFFELY GRNFNYLKTG IRIKEGGAYI AKEEIMKAMT
460 470 480 490 500
SGYRPSMLCI EDPLLPGNDV GRSSYGAMQV KQVFDYAYIV LSHAVSPLAR
510 520 530 540 550
SYPNRDAEST LGRIIKVTQE VIDYRRWIKE KWGSKAHPSP GMDSRIKIKE
560 570 580 590 600
RIATCNGEQT QNREPESPYG QRLTLSLSSP QLLSSGSSAS SVSSLSGSDV
610 620 630 640 650
DSDTPPCTTP SVYQFSLQAP APLMAGLPTA LPMPSGKPQP TTSRTLIMTT
660 670 680 690 700
NNQTRFTIPP PTLGVAPVPC RQAGVEGTAS LKAVHHMSSP AIPSASPNPL
710 720 730 740 750
SSPHLYHKQH NGMKLSMKGS HGHTQGGGYS SVGSGGVRPP VGNRGHHQYN
760 770
RTGWRRKKHT HTRDSLPVSL SR
Length:772
Mass (Da):82,360
Last modified:February 19, 2014 - v3
Checksum:iA5EBEC15CA37689C
GO
Isoform 2 (identifier: Q5XG87-2) [UniParc]FASTAAdd to basket

Also known as: s

The sequence of this isoform differs from the canonical sequence as follows:
     1-230: Missing.

Note: Exhibits poor nucleotidyl transferase activity.
Show »
Length:542
Mass (Da):59,874
Checksum:i233DA7E2222C2FB0
GO

Sequence cautioni

The sequence AAD45198.1 differs from that shown. Reason: Frameshift at position 474. Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti556 – 5561N → S.1 Publication
Corresponds to variant rs28381415 [ dbSNP | Ensembl ].
VAR_021175
Natural varianti626 – 6261G → S.1 Publication
Corresponds to variant rs28381418 [ dbSNP | Ensembl ].
VAR_021176

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 230230Missing in isoform 2. 4 PublicationsVSP_053732Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF089896 mRNA. Translation: AAD45198.1. Sequence problems.
KC424495 mRNA. Translation: AGE92663.1.
AB005754 mRNA. Translation: BAA24434.2.
AY623114 Genomic DNA. Translation: AAT38110.1.
AK289857 mRNA. Translation: BAF82546.1.
CH471102 Genomic DNA. Translation: EAX08101.1.
BC084567 mRNA. Translation: AAH84567.2.
BC117137 mRNA. Translation: AAI17138.1.
BC126106 mRNA. Translation: AAI26107.1.
CCDSiCCDS3871.1. [Q5XG87-2]
RefSeqiNP_001165276.1. NM_001171805.1.
NP_001165277.1. NM_001171806.1.
NP_008930.1. NM_006999.4. [Q5XG87-2]
XP_011512248.1. XM_011513946.1. [Q5XG87-2]
XP_011512249.1. XM_011513947.1. [Q5XG87-2]
UniGeneiHs.481542.

Genome annotation databases

EnsembliENST00000631941; ENSP00000488642; ENSG00000112941. [Q5XG87-2]
GeneIDi11044.
KEGGihsa:11044.
UCSCiuc003jdx.1. human. [Q5XG87-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Web resourcesi

NIEHS-SNPs

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF089896 mRNA. Translation: AAD45198.1. Sequence problems.
KC424495 mRNA. Translation: AGE92663.1.
AB005754 mRNA. Translation: BAA24434.2.
AY623114 Genomic DNA. Translation: AAT38110.1.
AK289857 mRNA. Translation: BAF82546.1.
CH471102 Genomic DNA. Translation: EAX08101.1.
BC084567 mRNA. Translation: AAH84567.2.
BC117137 mRNA. Translation: AAI17138.1.
BC126106 mRNA. Translation: AAI26107.1.
CCDSiCCDS3871.1. [Q5XG87-2]
RefSeqiNP_001165276.1. NM_001171805.1.
NP_001165277.1. NM_001171806.1.
NP_008930.1. NM_006999.4. [Q5XG87-2]
XP_011512248.1. XM_011513946.1. [Q5XG87-2]
XP_011512249.1. XM_011513947.1. [Q5XG87-2]
UniGeneiHs.481542.

3D structure databases

ProteinModelPortaliQ5XG87.
SMRiQ5XG87. Positions 223-516.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116232. 4 interactions.
IntActiQ5XG87. 1 interaction.
MINTiMINT-2999333.
STRINGi9606.ENSP00000230859.

PTM databases

PhosphoSiteiQ5XG87.

Polymorphism and mutation databases

BioMutaiPAPD7.
DMDMi60392922.

Proteomic databases

EPDiQ5XG87.
MaxQBiQ5XG87.
PaxDbiQ5XG87.
PRIDEiQ5XG87.

Protocols and materials databases

DNASUi11044.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000631941; ENSP00000488642; ENSG00000112941. [Q5XG87-2]
GeneIDi11044.
KEGGihsa:11044.
UCSCiuc003jdx.1. human. [Q5XG87-1]

Organism-specific databases

CTDi11044.
GeneCardsiPAPD7.
HGNCiHGNC:16705. PAPD7.
HPAiHPA045487.
HPA046742.
MIMi605198. gene.
neXtProtiNX_Q5XG87.
PharmGKBiPA33523.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1906. Eukaryota.
COG5260. LUCA.
GeneTreeiENSGT00400000022055.
HOGENOMiHOG000290646.
HOVERGENiHBG053636.
InParanoidiQ5XG87.
KOiK03514.
OMAiHSGMKLS.
OrthoDBiEOG7X6KZP.
TreeFamiTF313939.

Miscellaneous databases

ChiTaRSiPAPD7. human.
GenomeRNAii11044.
NextBioi41972.
PROiQ5XG87.
SOURCEiSearch...

Gene expression databases

BgeeiQ5XG87.
CleanExiHS_POLS.
ExpressionAtlasiQ5XG87. baseline and differential.
GenevisibleiQ5XG87. HS.

Family and domain databases

InterProiIPR002058. PAP_assoc.
IPR002934. Polymerase_NTP_transf_dom.
[Graphical view]
PfamiPF01909. NTP_transf_2. 1 hit.
PF03828. PAP_assoc. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The topoisomerase-related function gene TRF4 affects cellular sensitivity to the antitumor agent camptothecin."
    Walowsky C., Fitzhugh D.J., Castano I.B., Ju J.Y., Levin N.A., Christman M.F.
    J. Biol. Chem. 274:7302-7308(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
  2. "Molecular cloning and characterization of a novel isoform of the non-canonical poly(A) polymerase PAPD7."
    Ogami K., Cho R., Hoshino S.
    Biochem. Biophys. Res. Commun. 432:135-140(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF 167-ARG--PHE-230, ALTERNATIVE SPLICING.
  3. "mLT positive LAK-cell clone No. 1."
    Abe Y., Takaoka Y.
    Submitted (JUL-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
  4. NIEHS SNPs program
    Submitted (MAY-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS SER-556 AND SER-626.
  5. "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.
    , 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] (ISOFORM 2).
    Tissue: Brain.
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  7. "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 2).
    Tissue: Cerebellum and Lung.
  8. "Pol kappa: a DNA polymerase required for sister chromatid cohesion."
    Wang Z., Castano I.B., De Las Penas A., Adams C., Christman M.F.
    Science 289:774-779(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: PRELIMINARY FUNCTION.
  9. "Evidence that replication fork components catalyze establishment of cohesion between sister chromatids."
    Carson D.R., Christman M.F.
    Proc. Natl. Acad. Sci. U.S.A. 98:8270-8275(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  10. "Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'."
    Mullen T.E., Marzluff W.F.
    Genes Dev. 22:50-65(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: ABSENCE OF FUNCTION IN HISTONE MRNA DEGRADATION ACTIVITY.
  11. "Comparison of the yeast and human nuclear exosome complexes."
    Sloan K.E., Schneider C., Watkins N.J.
    Biochem. Soc. Trans. 40:850-855(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW ON RNA EXOSOMES.

Entry informationi

Entry nameiPAPD7_HUMAN
AccessioniPrimary (citable) accession number: Q5XG87
Secondary accession number(s): A8K1E2
, M1JCE6, O43289, Q17RZ1, Q9Y6C1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 2005
Last sequence update: February 19, 2014
Last modified: May 11, 2016
This is version 110 of the entry and version 3 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

Caution

Was originally thought to have DNA polymerase activity.Curated

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 5
    Human chromosome 5: 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. 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.