ID   UBP28_CHICK             Reviewed;        1047 AA.
AC   Q5ZID5;
DT   13-SEP-2005, integrated into UniProtKB/Swiss-Prot.
DT   23-NOV-2004, sequence version 1.
DT   27-MAR-2024, entry version 98.
DE   RecName: Full=Ubiquitin carboxyl-terminal hydrolase 28;
DE            EC=3.4.19.12;
DE   AltName: Full=Deubiquitinating enzyme 28;
DE   AltName: Full=Ubiquitin thioesterase 28;
DE   AltName: Full=Ubiquitin-specific-processing protease 28;
GN   Name=USP28; ORFNames=RCJMB04_27l24;
OS   Gallus gallus (Chicken).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC   Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae;
OC   Phasianinae; Gallus.
OX   NCBI_TaxID=9031;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=CB; TISSUE=Bursa of Fabricius;
RX   PubMed=15642098; DOI=10.1186/gb-2004-6-1-r6;
RA   Caldwell R.B., Kierzek A.M., Arakawa H., Bezzubov Y., Zaim J., Fiedler P.,
RA   Kutter S., Blagodatski A., Kostovska D., Koter M., Plachy J., Carninci P.,
RA   Hayashizaki Y., Buerstedde J.-M.;
RT   "Full-length cDNAs from chicken bursal lymphocytes to facilitate gene
RT   function analysis.";
RL   Genome Biol. 6:R6.1-R6.9(2005).
CC   -!- FUNCTION: Deubiquitinase involved in DNA damage response checkpoint and
CC       MYC proto-oncogene stability. Involved in DNA damage induced apoptosis
CC       by specifically deubiquitinating proteins of the DNA damage pathway
CC       such as CLSPN. Also involved in G2 DNA damage checkpoint, by
CC       deubiquitinating CLSPN, and preventing its degradation by the anaphase
CC       promoting complex/cyclosome (APC/C). Specifically deubiquitinates MYC
CC       in the nucleoplasm, leading to prevent MYC degradation by the
CC       proteasome. Deubiquitinates ZNF304, hence may prevent ZNF304
CC       degradation by the proteasome, leading to the activated KRAS-mediated
CC       promoter hypermethylation and transcriptional silencing of tumor
CC       suppressor genes (TSGs). {ECO:0000250|UniProtKB:Q96RU2}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide
CC         and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-
CC         residue protein attached to proteins as an intracellular targeting
CC         signal).; EC=3.4.19.12;
CC   -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the peptidase C19 family. USP28 subfamily.
CC       {ECO:0000305}.
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DR   EMBL; AJ720849; CAG32508.1; -; mRNA.
DR   RefSeq; NP_001026667.1; NM_001031496.1.
DR   AlphaFoldDB; Q5ZID5; -.
DR   SMR; Q5ZID5; -.
DR   STRING; 9031.ENSGALP00000044350; -.
DR   MEROPS; C19.054; -.
DR   PaxDb; 9031-ENSGALP00000011273; -.
DR   GeneID; 428246; -.
DR   KEGG; gga:428246; -.
DR   CTD; 57646; -.
DR   VEuPathDB; HostDB:geneid_428246; -.
DR   eggNOG; KOG1863; Eukaryota.
DR   InParanoid; Q5ZID5; -.
DR   PhylomeDB; Q5ZID5; -.
DR   PRO; PR:Q5ZID5; -.
DR   Proteomes; UP000000539; Unassembled WGS sequence.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR   GO; GO:0005654; C:nucleoplasm; ISS:UniProtKB.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0004843; F:cysteine-type deubiquitinase activity; ISS:UniProtKB.
DR   GO; GO:0008283; P:cell population proliferation; ISS:UniProtKB.
DR   GO; GO:0000077; P:DNA damage checkpoint signaling; ISS:UniProtKB.
DR   GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR   GO; GO:0042771; P:intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator; ISS:UniProtKB.
DR   GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR   GO; GO:0016579; P:protein deubiquitination; ISS:UniProtKB.
DR   GO; GO:0031647; P:regulation of protein stability; ISS:UniProtKB.
DR   GO; GO:0010212; P:response to ionizing radiation; ISS:UniProtKB.
DR   CDD; cd02665; Peptidase_C19I; 1.
DR   CDD; cd14355; UBA_UBP28; 1.
DR   CDD; cd20487; USP28_C; 1.
DR   Gene3D; 3.90.70.10; Cysteine proteinases; 1.
DR   Gene3D; 1.10.8.10; DNA helicase RuvA subunit, C-terminal domain; 1.
DR   InterPro; IPR038765; Papain-like_cys_pep_sf.
DR   InterPro; IPR001394; Peptidase_C19_UCH.
DR   InterPro; IPR009060; UBA-like_sf.
DR   InterPro; IPR044635; UBP14-like.
DR   InterPro; IPR018200; USP_CS.
DR   InterPro; IPR028889; USP_dom.
DR   PANTHER; PTHR43982; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE; 1.
DR   PANTHER; PTHR43982:SF6; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 2-RELATED; 1.
DR   Pfam; PF00443; UCH; 1.
DR   SUPFAM; SSF54001; Cysteine proteinases; 1.
DR   SUPFAM; SSF46934; UBA-like; 1.
DR   PROSITE; PS00972; USP_1; 1.
DR   PROSITE; PS00973; USP_2; 1.
DR   PROSITE; PS50235; USP_3; 1.
PE   2: Evidence at transcript level;
KW   DNA damage; DNA repair; Hydrolase; Nucleus; Protease; Reference proteome;
KW   Thiol protease; Ubl conjugation pathway.
FT   CHAIN           1..1047
FT                   /note="Ubiquitin carboxyl-terminal hydrolase 28"
FT                   /id="PRO_0000080659"
FT   DOMAIN          94..113
FT                   /note="UIM"
FT                   /evidence="ECO:0000305"
FT   DOMAIN          156..651
FT                   /note="USP"
FT   REGION          60..95
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          110..138
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          461..528
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          694..735
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        114..138
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        461..483
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        503..517
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        704..718
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        165
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
FT   ACT_SITE        601
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
SQ   SEQUENCE   1047 AA;  118747 MW;  93B40127861B2A00 CRC64;
     MTAELQAASG GPGGLEADCQ VLNKMKEITG IQDADFLHAA LKAAKGNLME ALIVLTEERD
     QEPVQNTAAA EPSSWEGSAV GKEPPQGGAA FDPEKKGDVH SAVAYGQLES PKAHAAERPQ
     EVHSPEHKNR SKRKRCEVWG ENSKQSDWKR VGDWPVGMKN IGNTCWFSAV IQSLFQLPQF
     RRLVLSYSFP PNVLESCRTR TGKRNIAFMQ ELQCLFALML GTRRKFVDPS AALELLRDAF
     KSTEEQQQDV SEFTHKLLDW LEDAFQLAVN VRSPGDKSEN PMVQLFYGTF LTEGVHEGNT
     FSKIETFGQY PLQVNGYRNL NECLEGAMVE GEMDEETATQ SVKYVQERWF TKLPPVLTFE
     LSRFEFNQSL GQPEKIHTKL EFPQTIFMDR YLYCSKELIQ TKREEMKKLK EKMLVLQQKL
     ERYMKYGSGP ARFPLPDMLQ YVLEFITTKP AGAVSSACVS STEDSQMMDR QSQGESLILG
     TPSQPDSMLD GKDGKPEDEA VLLANSSPQQ QLNAPLQPSE PPAEMSDCPA PHVVSEEEMN
     LVTTCLQRWR NEIEQDVRDL KESIARVSLS IDEMYSDPHL QQVPYHLHAV LVHEGQANAG
     HYWAFIYDQP RKSWLKYNDI SVTESSWEEL ERDSFGGLRN ASAYCLMYIS DKVSHVVAGE
     GDGSEVGQFQ KEVEALPPEL RRYIQEDNWR LEQEAEEWEE EQSCKIPSTA SESQELSPES
     GLDPPAAHEQ SLRSLSSEHA MIAKEQTAKA IANAANVYEK NGVEAALCEA FHEEYSRLYL
     LSKETPTPQN DARLQHVLVY FLQNDAPQQI VERTLLEQFA DKNLSYDERS ISIMKVARDK
     LKEIGPDEVN MEEYKKWHED YSLFRKVSVY LLTGLELYQN RKYKESLTYL IYAYQSNTTL
     LKKGANRGVN ESLITLYRRK CLLKLNEVAS SLFVSCEEAH VAEGISILNE LIIPCMHLIN
     NFDISREDMD AIEVMRNRWC SYLGREDMDA SLQIRLGELL PRLLDGSTEV VVLKEPPKIR
     PNSPYDLCSR FAAVMESIHD ASTVTVK
//