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TRAIP_XENLA
ID   TRAIP_XENLA             Reviewed;         464 AA.
AC   Q6NRV0; A0A1L8GP65;
DT   02-DEC-2020, integrated into UniProtKB/Swiss-Prot.
DT   02-DEC-2020, sequence version 2.
DT   03-AUG-2022, entry version 104.
DE   RecName: Full=E3 ubiquitin-protein ligase TRAIP {ECO:0000305};
DE            EC=2.3.2.27 {ECO:0000269|PubMed:30842657, ECO:0000269|PubMed:30979826};
DE   AltName: Full=TRAF-interacting protein {ECO:0000303|PubMed:30842657};
GN   Name=traip {ECO:0000303|PubMed:30842657};
GN   ORFNames=XELAEV_18023818mg {ECO:0000312|EMBL:OCT85647.1};
OS   Xenopus laevis (African clawed frog).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC   Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus.
OX   NCBI_TaxID=8355;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Embryo {ECO:0000312|EMBL:AAH70612.1};
RG   NIH - Xenopus Gene Collection (XGC) project;
RL   Submitted (MAY-2004) to the EMBL/GenBank/DDBJ databases.
RN   [2] {ECO:0000312|Proteomes:UP000186698}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=J;
RX   PubMed=27762356; DOI=10.1038/nature19840;
RA   Session A.M., Uno Y., Kwon T., Chapman J.A., Toyoda A., Takahashi S.,
RA   Fukui A., Hikosaka A., Suzuki A., Kondo M., van Heeringen S.J., Quigley I.,
RA   Heinz S., Ogino H., Ochi H., Hellsten U., Lyons J.B., Simakov O.,
RA   Putnam N., Stites J., Kuroki Y., Tanaka T., Michiue T., Watanabe M.,
RA   Bogdanovic O., Lister R., Georgiou G., Paranjpe S.S., van Kruijsbergen I.,
RA   Shu S., Carlson J., Kinoshita T., Ohta Y., Mawaribuchi S., Jenkins J.,
RA   Grimwood J., Schmutz J., Mitros T., Mozaffari S.V., Suzuki Y., Haramoto Y.,
RA   Yamamoto T.S., Takagi C., Heald R., Miller K., Haudenschild C., Kitzman J.,
RA   Nakayama T., Izutsu Y., Robert J., Fortriede J., Burns K., Lotay V.,
RA   Karimi K., Yasuoka Y., Dichmann D.S., Flajnik M.F., Houston D.W.,
RA   Shendure J., DuPasquier L., Vize P.D., Zorn A.M., Ito M., Marcotte E.M.,
RA   Wallingford J.B., Ito Y., Asashima M., Ueno N., Matsuda Y., Veenstra G.J.,
RA   Fujiyama A., Harland R.M., Taira M., Rokhsar D.S.;
RT   "Genome evolution in the allotetraploid frog Xenopus laevis.";
RL   Nature 538:336-343(2016).
RN   [3]
RP   SUBCELLULAR LOCATION.
RX   PubMed=26711499; DOI=10.1083/jcb.201506071;
RA   Hoffmann S., Smedegaard S., Nakamura K., Mortuza G.B., Raschle M.,
RA   Ibanez de Opakua A., Oka Y., Feng Y., Blanco F.J., Mann M., Montoya G.,
RA   Groth A., Bekker-Jensen S., Mailand N.;
RT   "TRAIP is a PCNA-binding ubiquitin ligase that protects genome stability
RT   after replication stress.";
RL   J. Cell Biol. 212:63-75(2016).
RN   [4]
RP   FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF CYS-25.
RX   PubMed=30979826; DOI=10.26508/lsa.201900390;
RA   Priego Moreno S., Jones R.M., Poovathumkadavil D., Scaramuzza S.,
RA   Gambus A.;
RT   "Mitotic replisome disassembly depends on TRAIP ubiquitin ligase
RT   activity.";
RL   Life. Sci Alliance 2:0-0(2019).
RN   [5]
RP   FUNCTION, AND MUTAGENESIS OF ARG-18 AND 456-GLN--LYS-464.
RX   PubMed=30849395; DOI=10.1016/j.molcel.2018.12.021;
RA   Deng L., Wu R.A., Sonneville R., Kochenova O.V., Labib K., Pellman D.,
RA   Walter J.C.;
RT   "Mitotic CDK Promotes replisome disassembly, fork breakage, and complex DNA
RT   rearrangements.";
RL   Mol. Cell 73:915-929(2019).
RN   [6]
RP   FUNCTION, SUBCELLULAR LOCATION, AND MUTAGENESIS OF ARG-18 AND
RP   456-GLN--LYS-464.
RX   PubMed=30842657; DOI=10.1038/s41586-019-1002-0;
RA   Wu R.A., Semlow D.R., Kamimae-Lanning A.N., Kochenova O.V., Chistol G.,
RA   Hodskinson M.R., Amunugama R., Sparks J.L., Wang M., Deng L., Mimoso C.A.,
RA   Low E., Patel K.J., Walter J.C.;
RT   "TRAIP is a master regulator of DNA interstrand crosslink repair.";
RL   Nature 567:267-272(2019).
RN   [7]
RP   FUNCTION, AND MUTAGENESIS OF ARG-18.
RX   PubMed=30595436; DOI=10.1016/j.molcel.2018.11.024;
RA   Larsen N.B., Gao A.O., Sparks J.L., Gallina I., Wu R.A., Mann M.,
RA   Raeschle M., Walter J.C., Duxin J.P.;
RT   "Replication-coupled DNA-protein crosslink repair by SPRTN and the
RT   proteasome in Xenopus egg extracts.";
RL   Mol. Cell 73:574-588(2019).
CC   -!- FUNCTION: E3 ubiquitin ligase required to protect genome stability in
CC       response to replication stress (PubMed:30979826, PubMed:30849395,
CC       PubMed:30842657). Acts as a key regulator of interstrand cross-link
CC       repair, which takes place when both strands of duplex DNA are
CC       covalently tethered together, thereby blocking replication and
CC       transcription (PubMed:30979826, PubMed:30849395, PubMed:30842657).
CC       Controls the choice between the two pathways of replication-coupled
CC       interstrand-cross-link repair by mediating ubiquitination of mcm7
CC       subunit of the CMG helicase complex (PubMed:30842657). Short ubiquitin
CC       chains on mcm7 promote recruitment of DNA glycosylase neil3
CC       (PubMed:30842657). If the interstrand cross-link cannot be cleaved by
CC       neil3, the ubiquitin chains continue to grow on mcm7, promoting the
CC       unloading of the CMG helicase complex by the vcp/p97 ATPase, enabling
CC       the Fanconi anemia DNA repair pathway (PubMed:30979826,
CC       PubMed:30842657). Only catalyzes ubiquitination of mcm7 when forks
CC       converge (PubMed:30842657). Also involved in the repair of covalent
CC       DNA-protein cross-links (DPCs) during DNA synthesis: promotes
CC       ubiquitination of DPCs, leading to their degradation by the proteasome
CC       (PubMed:30595436). Also acts as a negative regulator of innate immune
CC       signaling by inhibiting activation of NF-kappa-B mediated by TNF (By
CC       similarity). {ECO:0000250|UniProtKB:Q9BWF2,
CC       ECO:0000269|PubMed:30595436, ECO:0000269|PubMed:30842657,
CC       ECO:0000269|PubMed:30849395, ECO:0000269|PubMed:30979826}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine +
CC         [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-
CC         cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.;
CC         EC=2.3.2.27; Evidence={ECO:0000269|PubMed:30842657,
CC         ECO:0000269|PubMed:30979826};
CC   -!- PATHWAY: Protein modification; protein ubiquitination.
CC       {ECO:0000269|PubMed:30842657, ECO:0000269|PubMed:30979826}.
CC   -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC       {ECO:0000250|UniProtKB:Q9BWF2}. Nucleus, nucleolus
CC       {ECO:0000250|UniProtKB:Q9BWF2}. Chromosome
CC       {ECO:0000269|PubMed:26711499, ECO:0000269|PubMed:30842657,
CC       ECO:0000269|PubMed:30979826}. Cytoplasm {ECO:0000250|UniProtKB:Q9BWF2}.
CC       Note=Localizes to DNA damage sites in response to replication stress.
CC       {ECO:0000269|PubMed:26711499, ECO:0000269|PubMed:30842657}.
CC   -!- SIMILARITY: Belongs to the TRAIP family. {ECO:0000305}.
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DR   EMBL; CM004472; OCT85647.1; -; Genomic_DNA.
DR   EMBL; BC070612; AAH70612.1; -; mRNA.
DR   RefSeq; NP_001084838.1; NM_001091369.1.
DR   AlphaFoldDB; Q6NRV0; -.
DR   SMR; Q6NRV0; -.
DR   STRING; 8355.A0A1L8GP65; -.
DR   DNASU; 431884; -.
DR   GeneID; 431884; -.
DR   KEGG; xla:431884; -.
DR   CTD; 431884; -.
DR   Xenbase; XB-GENE-922331; traip.L.
DR   OMA; VMIRPLP; -.
DR   OrthoDB; 761263at2759; -.
DR   UniPathway; UPA00143; -.
DR   Proteomes; UP000186698; Chromosome 4L.
DR   Bgee; 431884; Expressed in egg cell and 19 other tissues.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005730; C:nucleolus; ISS:UniProtKB.
DR   GO; GO:0005654; C:nucleoplasm; ISS:UniProtKB.
DR   GO; GO:0090734; C:site of DNA damage; ISS:UniProtKB.
DR   GO; GO:1904931; F:MCM complex binding; IDA:UniProtKB.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0004842; F:ubiquitin-protein transferase activity; IDA:UniProtKB.
DR   GO; GO:0006974; P:cellular response to DNA damage stimulus; IDA:UniProtKB.
DR   GO; GO:0006281; P:DNA repair; IDA:UniProtKB.
DR   GO; GO:0036297; P:interstrand cross-link repair; IDA:UniProtKB.
DR   GO; GO:0016567; P:protein ubiquitination; IDA:UniProtKB.
DR   GO; GO:0106300; P:protein-DNA covalent cross-linking repair; IMP:UniProtKB.
DR   Gene3D; 3.30.40.10; -; 1.
DR   InterPro; IPR001841; Znf_RING.
DR   InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR   Pfam; PF13639; zf-RING_2; 1.
DR   SMART; SM00184; RING; 1.
DR   PROSITE; PS50089; ZF_RING_2; 1.
PE   1: Evidence at protein level;
KW   Chromosome; Coiled coil; Cytoplasm; DNA damage; DNA repair; Metal-binding;
KW   Nucleus; Reference proteome; Repeat; Transferase; Ubl conjugation pathway;
KW   Zinc; Zinc-finger.
FT   CHAIN           1..464
FT                   /note="E3 ubiquitin-protein ligase TRAIP"
FT                   /id="PRO_0000451420"
FT   ZN_FING         7..50
FT                   /note="RING-type; atypical"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT   REGION          439..464
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COILED          142..186
FT                   /evidence="ECO:0000255"
FT   COILED          236..277
FT                   /evidence="ECO:0000255"
FT   MOTIF           456..464
FT                   /note="PIP-box"
FT                   /evidence="ECO:0000269|PubMed:30842657"
FT   MUTAGEN         18
FT                   /note="R->C: Impaired ability to mediate ubiquitination of
FT                   mcm7. Abolished ability to promote ubiquitination of
FT                   covalent DNA-protein cross-links (DPCs)."
FT                   /evidence="ECO:0000269|PubMed:30595436,
FT                   ECO:0000269|PubMed:30842657, ECO:0000269|PubMed:30849395"
FT   MUTAGEN         25
FT                   /note="C->A: Abolished ability to mediate ubiquitination of
FT                   mcm7."
FT                   /evidence="ECO:0000269|PubMed:30979826"
FT   MUTAGEN         456..464
FT                   /note="Missing: Does not affect ability to mediate
FT                   ubiquitination of mcm7."
FT                   /evidence="ECO:0000269|PubMed:30842657,
FT                   ECO:0000269|PubMed:30849395"
FT   CONFLICT        17
FT                   /note="A -> T (in Ref. 1; AAH70612)"
SQ   SEQUENCE   464 AA;  52589 MW;  5708C5CB18F061CF CRC64;
     MPIRAYCTIC SDFFDNARDV AAITCGHTFH QECLLQWFHS APHRTCPQCR IQVSSRQIIN
     KLFFDIGGEE ETVLDAESLK NEVDRIKASL LVKEKEKREC QGLVDSLREM LDVRNVTIQS
     QQKELGDMEM LCSTLKKQIK FLDKQQSETK AAKDEARKLR NKLKTMESIE VLLQSQRSEV
     EEMIRDMGSG QAAVEQLAIY CVSLKKEYEN LKEVRKSSAE MTEKLRKELF SSNHKAQKAE
     LELTKVREEL SASQKELHSA DKEIMSLKKK VEFLQKTLTT PTASNEAISR LIFESPAPIG
     LERPKLRPPM MGNDINLDVT FDIDTPEHNT QKSVVAPFKK MKFDNKEHPL SSPTKNPLQE
     SKGLMSWAGG RTGADEDDDL TLPSFIKNSL LHKKPVGSLL GLRQNTGAVR TGFDGLGGRT
     KFIQPSNLTE IRPLHQKMKR KKVSRPTACT SSLANQPRLE DFLK
 
 
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