ID UBPH_CAEEL Reviewed; 1178 AA.
AC Q8WT44; G5EDU8;
DT 18-JUL-2018, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 27-MAR-2024, entry version 159.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase cyk-3 {ECO:0000305};
DE EC=3.4.19.12 {ECO:0000269|PubMed:11683918, ECO:0000269|PubMed:12006614};
DE AltName: Full=CeUBP130 {ECO:0000303|PubMed:11683918};
DE AltName: Full=Cytokinesis defective protein 3 {ECO:0000303|PubMed:12006614, ECO:0000312|WormBase:ZK328.1b};
GN Name=cyk-3 {ECO:0000303|PubMed:12006614, ECO:0000312|WormBase:ZK328.1b};
GN Synonyms=uch-1 {ECO:0000303|PubMed:11683918};
GN ORFNames=ZK328.1 {ECO:0000312|WormBase:ZK328.1b};
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM A), FUNCTION, CATALYTIC ACTIVITY, AND
RP MUTAGENESIS OF 98-GLN--LYS-1178.
RX PubMed=12006614; DOI=10.1242/jcs.115.11.2293;
RA Kaitna S., Schnabel H., Schnabel R., Hyman A.A., Glotzer M.;
RT "A ubiquitin C-terminal hydrolase is required to maintain osmotic balance
RT and execute actin-dependent processes in the early C. elegans embryo.";
RL J. Cell Sci. 115:2293-2302(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2 {ECO:0000312|Proteomes:UP000001940};
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, TISSUE SPECIFICITY,
RP DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF
RP 2-GLY--SER-255; 2-GLY--GLU-444 AND PHE-1135.
RX PubMed=11683918; DOI=10.1046/j.1365-2443.2001.00471.x;
RA Lee J., Jee C., Lee J.I., Lee M.H., Lee M.H., Koo H.S., Chung C.H.,
RA Ahnn J.;
RT "A deubiquitinating enzyme, UCH/CeUBP130, has an essential role in the
RT formation of a functional microtubule-organizing centre (MTOC) during early
RT cleavage in C. elegans.";
RL Genes Cells 6:899-911(2001).
RN [4]
RP FUNCTION.
RX PubMed=36476874; DOI=10.1016/j.celrep.2022.111653;
RA Hertel A., Alves L.M., Dutz H., Tascher G., Bonn F., Kaulich M., Dikic I.,
RA Eimer S., Steinberg F., Bremm A.;
RT "USP32-regulated LAMTOR1 ubiquitination impacts mTORC1 activation and
RT autophagy induction.";
RL Cell Rep. 41:111653-111653(2022).
CC -!- FUNCTION: Ubiquitin-protein hydrolase which cleaves ubiquitin from
CC ubiquitinated proteins (PubMed:12006614, PubMed:11683918). Plays a role
CC in embryo osmoregulation (PubMed:12006614). Probably by regulating
CC osmosis, controls actin redistribution in the 1-cell embryos and thus
CC actin-dependent processes such as cytokinesis and P-granules
CC segregation (PubMed:12006614, PubMed:11683918). During the first
CC embryonic mitotic division, involved in the formation of a functional
CC microtubule organizing center provided by the male pronucleus
CC (PubMed:11683918). Acts as a positive regulator of the mTORC1 signaling
CC (PubMed:36476874). {ECO:0000269|PubMed:11683918,
CC ECO:0000269|PubMed:12006614, ECO:0000269|PubMed:36476874}.
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; Evidence={ECO:0000269|PubMed:11683918,
CC ECO:0000269|PubMed:12006614};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:11683918}. Cytoplasm
CC {ECO:0000269|PubMed:11683918}. Cytoplasm, cytoskeleton, microtubule
CC organizing center {ECO:0000269|PubMed:11683918}. Note=At the 2-cell
CC stage embryo, localizes to the microtubule organizing center during
CC mitotic metaphase. Localizes to the cytoplasm in germ cells and sperm,
CC and to the nucleus in oocytes. {ECO:0000269|PubMed:11683918}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=b {ECO:0000312|WormBase:ZK328.1b};
CC IsoId=Q8WT44-1; Sequence=Displayed;
CC Name=a {ECO:0000312|WormBase:ZK328.1a};
CC IsoId=Q8WT44-2; Sequence=VSP_059638;
CC -!- TISSUE SPECIFICITY: Expressed in excretory cells, coelomocytes, head
CC neurons, hypodermal cells, germ cells, oocytes, sperm and pharynx (at
CC protein level). {ECO:0000269|PubMed:11683918}.
CC -!- DEVELOPMENTAL STAGE: Expressed in embryos and adults.
CC {ECO:0000269|PubMed:11683918}.
CC -!- DISRUPTION PHENOTYPE: RNAi-mediated knockdown causes embryonic
CC lethality. Embryos have impaired cleavage after fertilization and a
CC failure to form a functional paternal microtubule-organizing center
CC (MTOC). Due to a lack of cytokinesis, embryos become multinucleated.
CC {ECO:0000269|PubMed:11683918}.
CC -!- MISCELLANEOUS: Binds Ca(2+). {ECO:0000269|PubMed:11683918}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000255|PROSITE-
CC ProRule:PRU01035}.
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DR EMBL; AF469173; AAL79016.1; -; mRNA.
DR EMBL; BX284603; CCD70947.1; -; Genomic_DNA.
DR EMBL; BX284603; CCD70948.1; -; Genomic_DNA.
DR RefSeq; NP_001022992.1; NM_001027821.3. [Q8WT44-1]
DR RefSeq; NP_498311.2; NM_065910.6. [Q8WT44-2]
DR AlphaFoldDB; Q8WT44; -.
DR IntAct; Q8WT44; 3.
DR STRING; 6239.ZK328.1b.1; -.
DR MEROPS; C19.A44; -.
DR EPD; Q8WT44; -.
DR PaxDb; 6239-ZK328-1b; -.
DR EnsemblMetazoa; ZK328.1a.1; ZK328.1a.1; WBGene00000874. [Q8WT44-2]
DR EnsemblMetazoa; ZK328.1b.1; ZK328.1b.1; WBGene00000874. [Q8WT44-1]
DR GeneID; 175853; -.
DR KEGG; cel:CELE_ZK328.1; -.
DR UCSC; ZK328.1b; c. elegans. [Q8WT44-1]
DR AGR; WB:WBGene00000874; -.
DR WormBase; ZK328.1a; CE30061; WBGene00000874; cyk-3. [Q8WT44-2]
DR WormBase; ZK328.1b; CE30062; WBGene00000874; cyk-3. [Q8WT44-1]
DR eggNOG; KOG1870; Eukaryota.
DR GeneTree; ENSGT00990000209826; -.
DR HOGENOM; CLU_001060_10_1_1; -.
DR InParanoid; Q8WT44; -.
DR OMA; HICLGLR; -.
DR OrthoDB; 5474185at2759; -.
DR PhylomeDB; Q8WT44; -.
DR Reactome; R-CEL-5689880; Ub-specific processing proteases.
DR PRO; PR:Q8WT44; -.
DR Proteomes; UP000001940; Chromosome III.
DR Bgee; WBGene00000874; Expressed in pharyngeal muscle cell (C elegans) and 4 other cell types or tissues.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005815; C:microtubule organizing center; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0005509; F:calcium ion binding; IEA:InterPro.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IDA:UniProtKB.
DR GO; GO:0009792; P:embryo development ending in birth or egg hatching; IMP:UniProtKB.
DR GO; GO:0030010; P:establishment of cell polarity; IMP:UniProtKB.
DR GO; GO:0009992; P:intracellular water homeostasis; IMP:UniProtKB.
DR GO; GO:0031023; P:microtubule organizing center organization; IMP:UniProtKB.
DR GO; GO:1903673; P:mitotic cleavage furrow formation; IMP:UniProtKB.
DR GO; GO:1904263; P:positive regulation of TORC1 signaling; IMP:UniProtKB.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:1904785; P:regulation of asymmetric protein localization involved in cell fate determination; IMP:UniProtKB.
DR CDD; cd02674; Peptidase_C19R; 1.
DR Gene3D; 3.90.70.10; Cysteine proteinases; 2.
DR Gene3D; 3.30.2230.10; DUSP-like; 1.
DR Gene3D; 1.10.238.10; EF-hand; 1.
DR InterPro; IPR035927; DUSP-like_sf.
DR InterPro; IPR011992; EF-hand-dom_pair.
DR InterPro; IPR018247; EF_Hand_1_Ca_BS.
DR InterPro; IPR002048; EF_hand_dom.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR006615; Pept_C19_DUSP.
DR InterPro; IPR001394; Peptidase_C19_UCH.
DR InterPro; IPR028889; USP_dom.
DR PANTHER; PTHR21646; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE; 1.
DR PANTHER; PTHR21646:SF76; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 32; 1.
DR Pfam; PF06337; DUSP; 1.
DR Pfam; PF00443; UCH; 1.
DR SMART; SM00695; DUSP; 1.
DR SMART; SM00054; EFh; 2.
DR SUPFAM; SSF54001; Cysteine proteinases; 1.
DR SUPFAM; SSF143791; DUSP-like; 1.
DR SUPFAM; SSF47473; EF-hand; 2.
DR PROSITE; PS51283; DUSP; 1.
DR PROSITE; PS00018; EF_HAND_1; 2.
DR PROSITE; PS50222; EF_HAND_2; 3.
DR PROSITE; PS50235; USP_3; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Calcium; Cytoplasm; Cytoskeleton; Hydrolase;
KW Metal-binding; Nucleus; Protease; Reference proteome; Repeat;
KW Thiol protease; Ubl conjugation pathway.
FT CHAIN 1..1178
FT /note="Ubiquitin carboxyl-terminal hydrolase cyk-3"
FT /id="PRO_0000444675"
FT DOMAIN 28..60
FT /note="EF-hand 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT DOMAIN 175..210
FT /note="EF-hand 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT DOMAIN 211..246
FT /note="EF-hand 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT DOMAIN 296..410
FT /note="DUSP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00613"
FT DOMAIN 570..1175
FT /note="USP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01035"
FT REGION 681..725
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 686..725
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 579
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01035"
FT ACT_SITE 1134
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01035"
FT BINDING 188
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 190
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 192
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 194
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 199
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 224
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 226
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 228
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 235
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT VAR_SEQ 561..563
FT /note="Missing (in isoform a)"
FT /evidence="ECO:0000305"
FT /id="VSP_059638"
FT MUTAGEN 2..444
FT /note="Missing: Lacks catalytic activity in vitro.
FT Catalytic activity is restored; when associated with Y-
FT 1135."
FT /evidence="ECO:0000269|PubMed:11683918"
FT MUTAGEN 2..255
FT /note="Missing: Lacks catalytic activity in vitro.
FT Catalytic activity is restored; when associated with Y-
FT 1135."
FT /evidence="ECO:0000269|PubMed:11683918"
FT MUTAGEN 98..1178
FT /note="Missing: Cytokinesis is impaired during the
FT embryonic first mitotic division. Specifically, lacks
FT membrane contraction and pseudocleavage. Fails to extrude
FT polar bodies. Fails to segregate P-granules to the
FT posterior cortex. Redistribution of cortical actin to form
FT an anterior actin cap after pronuclear migration is
FT impaired as well as the actin-myosin-mediated polarization
FT of yolk granules. During late anaphase, the formation of
FT actin contractile ring is partially impaired. Impaired
FT osmoregulation causing embryos to swell."
FT /evidence="ECO:0000269|PubMed:12006614"
FT MUTAGEN 1135
FT /note="F->Y: Catalytic activity is restored; when
FT associated with 2-G-S-255 DEL or 2-G-E-444 DEL."
FT /evidence="ECO:0000269|PubMed:11683918"
SQ SEQUENCE 1178 AA; 134123 MW; 34F1FBA55DF4B6CA CRC64;
MGNTLTGRSN AIAPIISAED AKTYISDEEY RRIRQAFQRF KNGCINYDEF CYHVLGGAQI
PEEKRRLLFS FFSHGAETIS FDNLLSSLVG LCRVEEVQSR FIEEYHEFAS WGLSPPKLTI
PLNDSYISFY EVMSYVTHLS VNEVIELEKV FATISDRAVC KLNEEKWKQA LGGCFPDSYA
ERLFAVFDEN RDGQIDFREL VCTLSALCRG PLPGRISQLA RIWDVDCDKL LSDEELSNMY
KDLNVPEEHQ TVTKSSNGKS ALVDFGIWAQ ENEKYVNEYY SMALQIGHIC LGLRPESRKM
ELQIVNEFEK RASELPLSEW NIVASGWHAE LRSFLEADKN PNPIDNSGIK GTREDSWTSK
VACISAESAR LKPDLIPSDY IRVPVPLWRA WLRWHGCALT VDSQFTRKYL DGEFFEDNKP
ALELYPLEIL LLGHDRKKSQ DGTENTPRSL TSWACAQVSR SMTVDELLAL CKTELRLGDG
DARLWQVVKE NEEGNVLLDD GAQNLHQLYS SLGKTKKVNK MKLLLEVRER GTGVWPEELR
ASLSGKQITA ASTLSSNAQL SDSSGRPGAV GLVNYGNFCY RNAGIQCLAR VSPLTQYFLD
EDNLDAIKRG NLRRGDAAET TIEYAKLLRE MWAAKKKNIA PNDFNDAIRL SSDMFECSEQ
HDCQEFVAFL LDQLHTSMYE SNKSLHPSPE ESEGTDSNKL SDSSKKKEAD KEEADEEKAE
RSWTEYEKQN ESLVTQLFTG QLRSRLICRT CQSSSSVFEP FTSLSLPIGF EDVDLYQVIV
VHRDGRIPRR YGFRLSRDSK VGNLREVVAV SSGISMSHLT IQCMSSKGTL MSRSPNHRSS
NLRDELPLSS FPSGARLYAL ELPESTGEDQ WRVAMHRKLQ YNHEPYILGS TAGFIVSRFG
LPLIVGLDEE VTGKKLYEDV MYQMHRFMEH SVNSSSSRAH DPCEDENSGY PFTLCLVDPN
YEWCGQCPAL RFCRGCPIRP DESKVFIPAN CPIAVDWLPI ALYLRYNHSQ EQACEDDPSV
AETWSRHFAP SSLEHCIEKF SCPETLDAAI QCDRCEKKTM RDKVMTIWKL PKYLIIHLKR
FEFLREQGRM GKCKRTVNFP LKHFDPAPFV DKPDGNTYEC IALANHYGQL SCGHFIAYAK
SNEDKWLLLN DCSVREVSEE EVDKQGAYLL FYERKDVK
//
