UBP14_ARATH
ID UBP14_ARATH Reviewed; 797 AA.
AC Q8L6Y1; Q0WV77; Q9FPT0; Q9LJT6;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 14;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme 14;
DE Short=AtUBP14;
DE AltName: Full=TITAN-6 protein;
DE AltName: Full=Ubiquitin thioesterase 14;
DE AltName: Full=Ubiquitin-specific-processing protease 14;
GN Name=UBP14; Synonyms=TTN6; OrderedLocusNames=At3g20630;
GN ORFNames=F3H11_1, K10D20.17, K10D20.26;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], GENE FAMILY ORGANIZATION, AND NOMENCLATURE.
RC STRAIN=cv. Columbia;
RX PubMed=11115897; DOI=10.1104/pp.124.4.1828;
RA Yan N., Doelling J.H., Falbel T.G., Durski A.M., Vierstra R.D.;
RT "The ubiquitin-specific protease family from Arabidopsis. AtUBP1 and 2 are
RT required for the resistance to the amino acid analog canavanine.";
RL Plant Physiol. 124:1828-1843(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=11576424; DOI=10.1046/j.1365-313x.2001.01106.x;
RA Doelling J.H., Yan N., Kurepa J., Walker J., Vierstra R.D.;
RT "The ubiquitin-specific protease UBP14 is essential for early embryo
RT development in Arabidopsis thaliana.";
RL Plant J. 27:393-405(2001).
RN [7]
RP FUNCTION.
RX PubMed=11788751; DOI=10.1104/pp.010911;
RA Tzafrir I., McElver J.A., Liu C.-M., Yang L.J., Wu J.Q., Martinez A.,
RA Patton D.A., Meinke D.W.;
RT "Diversity of TITAN functions in Arabidopsis seed development.";
RL Plant Physiol. 128:38-51(2002).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=17272265; DOI=10.1074/mcp.m600408-mcp200;
RA Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
RT "Multidimensional protein identification technology (MudPIT) analysis of
RT ubiquitinated proteins in plants.";
RL Mol. Cell. Proteomics 6:601-610(2007).
RN [9]
RP STRUCTURE BY NMR OF 594-665.
RG RIKEN structural genomics initiative (RSGI);
RT "Solution structure of RSGI RUH-011, a UBA domain from Arabidopsis cDNA.";
RL Submitted (SEP-2004) to the PDB data bank.
RN [10]
RP STRUCTURE BY NMR OF 651-710.
RG RIKEN structural genomics initiative (RSGI);
RT "Solution structure of RSGI RUH-023, a UBA domain from Arabidopsis cDNA.";
RL Submitted (NOV-2004) to the PDB data bank.
CC -!- FUNCTION: Recognizes and hydrolyzes the peptide bond at the C-terminal
CC Gly of ubiquitin. Involved in the processing of poly-ubiquitin
CC precursors as well as that of ubiquitinated proteins. Involved in seed
CC and embryo development. {ECO:0000269|PubMed:11576424,
CC ECO:0000269|PubMed:11788751}.
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 -!- TISSUE SPECIFICITY: Constitutively and ubiquitously expressed (at
CC protein level). {ECO:0000269|PubMed:11576424}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR EMBL; AF302664; AAG42755.1; -; mRNA.
DR EMBL; AP000410; BAB01171.1; -; Genomic_DNA.
DR EMBL; AP002034; BAB01171.1; JOINED; Genomic_DNA.
DR EMBL; CP002686; AEE76405.1; -; Genomic_DNA.
DR EMBL; AY140096; AAM98237.1; -; mRNA.
DR EMBL; AK226894; BAE98971.1; -; mRNA.
DR RefSeq; NP_566666.2; NM_112954.4.
DR PDB; 1VEK; NMR; -; A=594-664.
DR PDB; 1WIV; NMR; -; A=651-710.
DR PDBsum; 1VEK; -.
DR PDBsum; 1WIV; -.
DR AlphaFoldDB; Q8L6Y1; -.
DR SMR; Q8L6Y1; -.
DR BioGRID; 6942; 10.
DR STRING; 3702.AT3G20630.1; -.
DR MEROPS; C19.084; -.
DR iPTMnet; Q8L6Y1; -.
DR PaxDb; Q8L6Y1; -.
DR PRIDE; Q8L6Y1; -.
DR ProteomicsDB; 233047; -.
DR DNASU; 821610; -.
DR EnsemblPlants; AT3G20630.1; AT3G20630.1; AT3G20630.
DR GeneID; 821610; -.
DR Gramene; AT3G20630.1; AT3G20630.1; AT3G20630.
DR KEGG; ath:AT3G20630; -.
DR Araport; AT3G20630; -.
DR TAIR; locus:2083440; AT3G20630.
DR eggNOG; KOG0944; Eukaryota.
DR HOGENOM; CLU_009884_1_0_1; -.
DR InParanoid; Q8L6Y1; -.
DR OMA; FDERQAV; -.
DR OrthoDB; 556111at2759; -.
DR PhylomeDB; Q8L6Y1; -.
DR EvolutionaryTrace; Q8L6Y1; -.
DR PRO; PR:Q8L6Y1; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q8L6Y1; baseline and differential.
DR Genevisible; Q8L6Y1; AT.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IDA:TAIR.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; IBA:GO_Central.
DR GO; GO:1990450; F:linear polyubiquitin binding; IDA:TAIR.
DR GO; GO:0061815; F:Met1-linked polyubiquitin deubiquitinase activity; IDA:TAIR.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0009734; P:auxin-activated signaling pathway; IMP:TAIR.
DR GO; GO:0071370; P:cellular response to gibberellin stimulus; IGI:TAIR.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
DR GO; GO:0009965; P:leaf morphogenesis; IMP:TAIR.
DR GO; GO:0016579; P:protein deubiquitination; IDA:TAIR.
DR GO; GO:0042127; P:regulation of cell population proliferation; IMP:TAIR.
DR GO; GO:0048767; P:root hair elongation; IMP:TAIR.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR Gene3D; 3.30.40.10; -; 2.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR001394; Peptidase_C19_UCH.
DR InterPro; IPR015940; UBA.
DR InterPro; IPR009060; UBA-like_sf.
DR InterPro; IPR016652; Ubiquitinyl_hydrolase.
DR InterPro; IPR041432; UBP13_Znf-UBP_var.
DR InterPro; IPR018200; USP_CS.
DR InterPro; IPR028889; USP_dom.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR InterPro; IPR001607; Znf_UBP.
DR Pfam; PF00627; UBA; 2.
DR Pfam; PF00443; UCH; 1.
DR Pfam; PF02148; zf-UBP; 1.
DR Pfam; PF17807; zf-UBP_var; 1.
DR PIRSF; PIRSF016308; UBP; 1.
DR SMART; SM00165; UBA; 2.
DR SMART; SM00290; ZnF_UBP; 1.
DR SUPFAM; SSF46934; SSF46934; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS50030; UBA; 2.
DR PROSITE; PS00972; USP_1; 1.
DR PROSITE; PS00973; USP_2; 1.
DR PROSITE; PS50235; USP_3; 1.
DR PROSITE; PS50271; ZF_UBP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Protease; Reference proteome;
KW Repeat; Thiol protease; Ubl conjugation pathway; Zinc; Zinc-finger.
FT CHAIN 1..797
FT /note="Ubiquitin carboxyl-terminal hydrolase 14"
FT /id="PRO_0000080697"
FT DOMAIN 308..796
FT /note="USP"
FT DOMAIN 613..654
FT /note="UBA 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT DOMAIN 670..710
FT /note="UBA 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT ZN_FING 156..266
FT /note="UBP-type; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT ACT_SITE 317
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT ACT_SITE 758
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT BINDING 180
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 183
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 200
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 213
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT CONFLICT 601
FT /note="G -> A (in Ref. 1; AAG42755)"
FT /evidence="ECO:0000305"
FT STRAND 603..605
FT /evidence="ECO:0007829|PDB:1VEK"
FT HELIX 616..625
FT /evidence="ECO:0007829|PDB:1VEK"
FT HELIX 629..638
FT /evidence="ECO:0007829|PDB:1VEK"
FT TURN 639..641
FT /evidence="ECO:0007829|PDB:1VEK"
FT HELIX 644..654
FT /evidence="ECO:0007829|PDB:1VEK"
FT TURN 659..661
FT /evidence="ECO:0007829|PDB:1VEK"
FT HELIX 673..682
FT /evidence="ECO:0007829|PDB:1WIV"
FT HELIX 686..695
FT /evidence="ECO:0007829|PDB:1WIV"
FT HELIX 700..709
FT /evidence="ECO:0007829|PDB:1WIV"
SQ SEQUENCE 797 AA; 88374 MW; B827C513A6D5C4E2 CRC64;
MELLRSNLSR VQIPEPTHRI YKHECCISFD TPRSEGGLFV DMNSFLAFGK DYVSWNYEKT
GNPVYLHIKQ TRKSIPEDRP LKKPTLLAIG VDGGFDNNEP EYEESYSIVI LPDFVSLPFP
SVELPEKVRI AVDTVVNAVG AERKEQVAAW TAEKKLISEH ALTLQQIKSG IVIPPSGWKC
SKCDKTENLW LNLTDGMILC GRKNWDGTGG NNHAVEHYKE TAYPLAVKLG TITADLEAAD
VYSYPEDDSV LDPLLAEHLA HFGIDFSSMQ KTEMTTAERE LDQNTNFDWN RIQESGKELV
PVFGPGYTGL VNLGNSCYLA ATMQIVFSTH SFISRYFSHQ SLKMAFEMAP ADPTLDLNMQ
LTKLGHGLLS GKYSMPATQK DATTGDPRQE GIPPRMFKNV IAASHAEFSS MRQQDALDFF
LHLVGKVERA SNTTPDLDPS RSFKFGIEEK ILCPSGKVGY NKREDCILSL NIPLHEATNK
DELEAFHKQK AGKGLEENDM RSSDEIVRPR VPLEACLANF ASSEPIEDYY SSALKGMTTA
IKTTGLTSFP DYLVLHMRKF VMEEGWVPKK LDVYIDVPDV IDISHMRSKG LQPGEELLPD
GVPEEVMESA QPVANEEIVA QLVSMGFSQL HCQKAAINTS NAGVEEAMNW LLSHMDDPDI
DAPISHQTSD IDQSSVDTLL SFGFAEDVAR KALKASGGDI EKATDWVFNN PNASVSDMDV
SSSNSAQTPA QSGLPDGGGK YKLFGIVSHM GTSVHCGHYV AHILKEGRWV IFNDDKVGIS
TDPPKDMGYV YFFQRLD
