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Protein

Ubiquitin carboxyl-terminal hydrolase 6

Gene

UBP6

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin. Involved in the processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins.

Catalytic activityi

Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei113 – 1131Nucleophile
Active sitei430 – 4301Proton acceptorPROSITE-ProRule annotation

GO - Molecular functioni

  1. calmodulin binding Source: TAIR
  2. cysteine-type endopeptidase activity Source: GO_Central
  3. ubiquitinyl hydrolase activity Source: InterPro

GO - Biological processi

  1. proteasome-mediated ubiquitin-dependent protein catabolic process Source: GO_Central
  2. protein deubiquitination Source: TAIR
  3. regulation of proteasomal protein catabolic process Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Keywords - Ligandi

Calmodulin-binding

Enzyme and pathway databases

BioCyciARA:AT1G51710-MONOMER.
ARA:GQT-1079-MONOMER.

Protein family/group databases

MEROPSiC19.094.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase 6 (EC:3.4.19.12)
Alternative name(s):
Deubiquitinating enzyme 6
Short name:
AtUBP6
Ubiquitin thioesterase 6
Ubiquitin-specific-processing protease 6
Gene namesi
Name:UBP6
Ordered Locus Names:At1g51710
ORF Names:F19C24.8
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G51710.

Subcellular locationi

GO - Cellular componenti

  1. plasmodesma Source: TAIR
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi113 – 1131C → S: Loss of activity. 1 Publication
Mutagenesisi175 – 1751W → R: Abolishes the calmodulin-binding. 1 Publication
Mutagenesisi178 – 1781L → K: Abolishes the calmodulin-binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 482482Ubiquitin carboxyl-terminal hydrolase 6PRO_0000313033Add
BLAST

Proteomic databases

PaxDbiQ949Y0.
PRIDEiQ949Y0.

Expressioni

Gene expression databases

ExpressionAtlasiQ949Y0. baseline and differential.
GenevestigatoriQ949Y0.

Interactioni

Subunit structurei

Interacts with calmodulin (CaM).1 Publication

Protein-protein interaction databases

BioGridi26821. 4 interactions.
MINTiMINT-1351065.

Structurei

3D structure databases

ProteinModelPortaliQ949Y0.
SMRiQ949Y0. Positions 4-478.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 7776Ubiquitin-likePROSITE-ProRule annotationAdd
BLAST
Domaini104 – 478375USPAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni172 – 19120Calmodulin-bindingAdd
BLAST

Sequence similaritiesi

Belongs to the peptidase C19 family.Curated
Contains 1 ubiquitin-like domain.PROSITE-ProRule annotation
Contains 1 USP domain.Curated

Phylogenomic databases

eggNOGiNOG286607.
HOGENOMiHOG000202292.
InParanoidiQ949Y0.
KOiK11843.
OMAiDWGNLKI.
PhylomeDBiQ949Y0.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR018200. USP_CS.
IPR028889. USP_dom.
[Graphical view]
PfamiPF00240. ubiquitin. 1 hit.
PF00443. UCH. 1 hit.
[Graphical view]
SMARTiSM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
PS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

This entry describes 1 isoform i produced by alternative splicing. AlignAdd to basket

Note: A number of isoforms are produced. According to EST sequences.

Isoform 1 (identifier: Q949Y0-1) [UniParc]FASTAAdd to basket

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
MPTVSVKWQK KVLDGIEIDV SLPPYVFKAQ LYDLTGVPPE RQKIMVKGGL
60 70 80 90 100
LKDDGDWAAI GVKDGQKLMM MGTADEIVKA PEKAIVFAED LPEEALATNL
110 120 130 140 150
GYSAGLVNLG NTCYMNSTVQ CLKSVPELKS ALSNYSLAAR SNDVDQTSHM
160 170 180 190 200
LTVATRELFG ELDRSVNAVS PSQFWMVLRK KYPQFSQLQN GMHMQQDAEE
210 220 230 240 250
CWTQLLYTLS QSLKAPTSSE GADAVKALFG VNLQSRLHCQ ESGEESSETE
260 270 280 290 300
SVYSLKCHIS HEVNHLHEGL KHGLKGELEK TSPALGRTAL YVKESLIDSL
310 320 330 340 350
PRYLTVQFVR FFWKRESNQK AKILRKVDYP LVLDIFDLCS EDLRKKLEAP
360 370 380 390 400
RQKLREEEGK KLGLQTSAKS GSKDSDVKMT DAEASANGSG ESSTVNPQEG
410 420 430 440 450
TSSEKETHMT GIYDLVAVLT HKGRSADSGH YVAWVKQESG KWIQYDDDNP
460 470 480
SMQREEDITK LSGGGDWHMA YITMYKARFV SM
Length:482
Mass (Da):53,696
Last modified:November 30, 2001 - v1
Checksum:iECF357E9C5BEF3F7
GO

Sequence cautioni

The sequence AAG50872.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti207 – 2071Y → F in AAG42751 (PubMed:11115897).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF302660 mRNA. Translation: AAG42751.1.
AC025294 Genomic DNA. Translation: AAG50872.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE32705.1.
AY050817 mRNA. Translation: AAK92752.1.
AY114081 mRNA. Translation: AAM45129.1.
BT000658 mRNA. Translation: AAN31805.1.
AY084730 mRNA. Translation: AAM61304.1.
AK221019 mRNA. Translation: BAD94710.1.
PIRiA96556.
RefSeqiNP_564596.1. NM_104049.3. [Q949Y0-1]
UniGeneiAt.16941.

Genome annotation databases

EnsemblPlantsiAT1G51710.1; AT1G51710.1; AT1G51710. [Q949Y0-1]
GeneIDi841596.
KEGGiath:AT1G51710.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF302660 mRNA. Translation: AAG42751.1.
AC025294 Genomic DNA. Translation: AAG50872.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE32705.1.
AY050817 mRNA. Translation: AAK92752.1.
AY114081 mRNA. Translation: AAM45129.1.
BT000658 mRNA. Translation: AAN31805.1.
AY084730 mRNA. Translation: AAM61304.1.
AK221019 mRNA. Translation: BAD94710.1.
PIRiA96556.
RefSeqiNP_564596.1. NM_104049.3. [Q949Y0-1]
UniGeneiAt.16941.

3D structure databases

ProteinModelPortaliQ949Y0.
SMRiQ949Y0. Positions 4-478.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi26821. 4 interactions.
MINTiMINT-1351065.

Protein family/group databases

MEROPSiC19.094.

Proteomic databases

PaxDbiQ949Y0.
PRIDEiQ949Y0.

Protocols and materials databases

DNASUi841596.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G51710.1; AT1G51710.1; AT1G51710. [Q949Y0-1]
GeneIDi841596.
KEGGiath:AT1G51710.

Organism-specific databases

TAIRiAT1G51710.

Phylogenomic databases

eggNOGiNOG286607.
HOGENOMiHOG000202292.
InParanoidiQ949Y0.
KOiK11843.
OMAiDWGNLKI.
PhylomeDBiQ949Y0.

Enzyme and pathway databases

BioCyciARA:AT1G51710-MONOMER.
ARA:GQT-1079-MONOMER.

Gene expression databases

ExpressionAtlasiQ949Y0. baseline and differential.
GenevestigatoriQ949Y0.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR018200. USP_CS.
IPR028889. USP_dom.
[Graphical view]
PfamiPF00240. ubiquitin. 1 hit.
PF00443. UCH. 1 hit.
[Graphical view]
SMARTiSM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
PS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The ubiquitin-specific protease family from Arabidopsis. AtUBP1 and 2 are required for the resistance to the amino acid analog canavanine."
    Yan N., Doelling J.H., Falbel T.G., Durski A.M., Vierstra R.D.
    Plant Physiol. 124:1828-1843(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], GENE FAMILY ORGANIZATION, NOMENCLATURE.
    Strain: cv. Columbia.
  2. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (MAR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Full-length cDNA from Arabidopsis thaliana."
    Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
    Submitted (FEB-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  6. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
    , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
    Submitted (FEB-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 336-482.
    Strain: cv. Columbia.
  7. "Arabidopsis ubiquitin-specific protease 6 (AtUBP6) interacts with calmodulin."
    Moon B.C., Choi M.S., Kang Y.H., Kim M.C., Cheong M.S., Park C.Y., Yoo J.H., Koo S.C., Lee S.M., Lim C.O., Cho M.J., Chung W.S.
    FEBS Lett. 579:3885-3890(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH CALMODULIN, MUTAGENESIS OF CYS-113; TRP-175 AND LEU-178.

Entry informationi

Entry nameiUBP6_ARATH
AccessioniPrimary (citable) accession number: Q949Y0
Secondary accession number(s): Q56ZE7, Q9C8H9, Q9FPT4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 14, 2008
Last sequence update: November 30, 2001
Last modified: March 31, 2015
This is version 96 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.