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Q84WU2

- UBP13_ARATH

UniProt

Q84WU2 - UBP13_ARATH

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Protein

Ubiquitin carboxyl-terminal hydrolase 13

Gene

UBP13

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 4 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 (By similarity).By similarity

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 sitei207 – 2071NucleophilePROSITE-ProRule annotation
Active sitei454 – 4541Proton acceptorPROSITE-ProRule annotation

GO - Molecular functioni

  1. cysteine-type peptidase activity Source: UniProtKB-KW
  2. ubiquitinyl hydrolase activity Source: InterPro

GO - Biological processi

  1. ubiquitin-dependent protein catabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Enzyme and pathway databases

BioCyciARA:AT3G11910-MONOMER.
ARA:GQT-2250-MONOMER.

Protein family/group databases

MEROPSiC19.A53.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase 13 (EC:3.4.19.12)
Alternative name(s):
Deubiquitinating enzyme 13
Short name:
AtUBP13
Ubiquitin thioesterase 13
Ubiquitin-specific-processing protease 13
Gene namesi
Name:UBP13
Ordered Locus Names:At3g11910
ORF Names:F26K24.20, MEC18.1
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 3

Organism-specific databases

TAIRiAT3G11910.

Subcellular locationi

GO - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11151115Ubiquitin carboxyl-terminal hydrolase 13PRO_0000313040Add
BLAST

Post-translational modificationi

Ubiquitinated.1 Publication

Keywords - PTMi

Ubl conjugation

Proteomic databases

PaxDbiQ84WU2.
PRIDEiQ84WU2.

Expressioni

Gene expression databases

ExpressionAtlasiQ84WU2. baseline and differential.
GenevestigatoriQ84WU2.

Interactioni

Protein-protein interaction databases

BioGridi5698. 3 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ84WU2.
SMRiQ84WU2. Positions 56-638.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini53 – 178126MATHPROSITE-ProRule annotationAdd
BLAST
Domaini198 – 522325USPAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG5077.
HOGENOMiHOG000160240.
InParanoidiQ84WU2.
KOiK11838.
OMAiEGERTIN.
PhylomeDBiQ84WU2.

Family and domain databases

InterProiIPR002083. MATH.
IPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR008974. TRAF-like.
IPR028889. UCH/PAN2.
IPR024729. USP7_ICP0-binding_dom.
IPR029346. USP_C.
[Graphical view]
PfamiPF00917. MATH. 1 hit.
PF00443. UCH. 1 hit.
PF14533. USP7_C2. 1 hit.
PF12436. USP7_ICP0_bdg. 1 hit.
[Graphical view]
SMARTiSM00061. MATH. 1 hit.
[Graphical view]
SUPFAMiSSF49599. SSF49599. 1 hit.
PROSITEiPS50144. MATH. 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. Align

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

Isoform 1 (identifier: Q84WU2-1) [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
MTMMTPPPLD QQEDEEMLVP NPDLVEGPQP MEVAQTDPAA TAVENPPPED
60 70 80 90 100
PPSLKFTWTI PMFTRLNTRK HYSDVFVVGG YKWRILIFPK GNNVDHLSMY
110 120 130 140 150
LDVADAANLP YGWSRYSQFS LAVVNQVNNR YSIRKETQHQ FNARESDWGF
160 170 180 190 200
TSFMPLSELY EPTRGYLVND TVLIEAEVAV RKVLDYWSYD SKKETGFVGL
210 220 230 240 250
KNQGATCYMN SLLQTLYHIP YFRKAVYHMP TTENDAPTAS IPLALQSLFY
260 270 280 290 300
KLQYNDTSVA TKELTKSFGW DTYDSFMQHD VQELNRVLCE KLEDKMKGTV
310 320 330 340 350
VEGTIQKLFE GHHMNYIECI NVDYKSTRKE SFYDLQLDVK GCKDVYASFD
360 370 380 390 400
KYVEVERLEG DNKYHAEGHD LQDAKKGVLF IDFPPVLQLQ LKRFEYDFMR
410 420 430 440 450
DTMVKINDRY EFPLQLDLDR EDGRYLSPDA DKSVRNLYTL HSVLVHSGGV
460 470 480 490 500
HGGHYYAFIR PTLSDQWYKF DDERVTKEDV KRALEEQYGG EEELPQNNPG
510 520 530 540 550
FNNPPFKFTK YSNAYMLVYI RESDKDKIIC NVDEKDIAEH LRVRLKKEQE
560 570 580 590 600
EKEDKRKYKA QAHLFTTIKV ARDDDITEQI GKNIYFDLVD HEKVRSFRIQ
610 620 630 640 650
KQTPFQQFKE EVAKEFGVPV QLQRFWIWAK RQNHTYRPNR PLSPNEELQT
660 670 680 690 700
VGQIREASNK ANNAELKLFL EIERGPDDLP IPPPEKTSED ILLFFKLYDP
710 720 730 740 750
ENAVLRYVGR LMVKSSSKPM DIVGQLNKMA GFAPDEEIEL FEEIKFEPCV
760 770 780 790 800
MCEQIDKKTS FRLCQIEDGD IICYQKPLSI EESEFRYPDV PSFLEYVQNR
810 820 830 840 850
ELVRFRTLEK PKEDEFTMEL SKLHTYDDVV ERVAEKLGLD DPSKLRLTSH
860 870 880 890 900
NCYSQQPKPQ PIKYRGVDHL SDMLVHYNQT SDILYYEVLD IPLPELQGLK
910 920 930 940 950
TLKVAFHSAT KDEVIIHNIR LPKQSTVGDV INELKTKVEL SHQDAELRLL
960 970 980 990 1000
EVFFHKIYKI FPSTERIENI NDQYWTLRAE EIPEEEKNIG PNDRLIHVYH
1010 1020 1030 1040 1050
FTKEAGQNQQ VQNFGEPFFL VIHEGETLEE IKTRIQKKLH VPDEDFAKWK
1060 1070 1080 1090 1100
FASFSMGRPD YLLDTDVVYN RFQRRDVYGA WEQYLGLEHI DNAPKRAYAA
1110
NQNRHAYEKP VKIYN
Length:1,115
Mass (Da):130,649
Last modified:June 1, 2003 - v1
Checksum:i29D3A53A60CCDFF1
GO

Sequence cautioni

The sequence AAF23207.1 differs from that shown. Reason: Erroneous gene model prediction.
The sequence BAB17021.1 differs from that shown. Reason: Erroneous gene model prediction.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AC016795 Genomic DNA. Translation: AAF23207.1. Sequence problems.
AP002040 Genomic DNA. Translation: BAB17021.1. Sequence problems.
CP002686 Genomic DNA. Translation: AEE75116.1.
BT002760 mRNA. Translation: AAO22588.1.
AK226819 mRNA. Translation: BAE98915.1.
RefSeqiNP_187797.3. NM_112024.5. [Q84WU2-1]
UniGeneiAt.25337.

Genome annotation databases

EnsemblPlantsiAT3G11910.1; AT3G11910.1; AT3G11910. [Q84WU2-1]
GeneIDi820364.
KEGGiath:AT3G11910.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AC016795 Genomic DNA. Translation: AAF23207.1 . Sequence problems.
AP002040 Genomic DNA. Translation: BAB17021.1 . Sequence problems.
CP002686 Genomic DNA. Translation: AEE75116.1 .
BT002760 mRNA. Translation: AAO22588.1 .
AK226819 mRNA. Translation: BAE98915.1 .
RefSeqi NP_187797.3. NM_112024.5. [Q84WU2-1 ]
UniGenei At.25337.

3D structure databases

ProteinModelPortali Q84WU2.
SMRi Q84WU2. Positions 56-638.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 5698. 3 interactions.

Protein family/group databases

MEROPSi C19.A53.

Proteomic databases

PaxDbi Q84WU2.
PRIDEi Q84WU2.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT3G11910.1 ; AT3G11910.1 ; AT3G11910 . [Q84WU2-1 ]
GeneIDi 820364.
KEGGi ath:AT3G11910.

Organism-specific databases

TAIRi AT3G11910.

Phylogenomic databases

eggNOGi COG5077.
HOGENOMi HOG000160240.
InParanoidi Q84WU2.
KOi K11838.
OMAi EGERTIN.
PhylomeDBi Q84WU2.

Enzyme and pathway databases

BioCyci ARA:AT3G11910-MONOMER.
ARA:GQT-2250-MONOMER.

Gene expression databases

ExpressionAtlasi Q84WU2. baseline and differential.
Genevestigatori Q84WU2.

Family and domain databases

InterProi IPR002083. MATH.
IPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR008974. TRAF-like.
IPR028889. UCH/PAN2.
IPR024729. USP7_ICP0-binding_dom.
IPR029346. USP_C.
[Graphical view ]
Pfami PF00917. MATH. 1 hit.
PF00443. UCH. 1 hit.
PF14533. USP7_C2. 1 hit.
PF12436. USP7_ICP0_bdg. 1 hit.
[Graphical view ]
SMARTi SM00061. MATH. 1 hit.
[Graphical view ]
SUPFAMi SSF49599. SSF49599. 1 hit.
PROSITEi PS50144. MATH. 1 hit.
PS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana."
    Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F.
    , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
    Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC clones."
    Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.
    DNA Res. 7:217-221(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "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 (JUL-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-545.
    Strain: cv. Columbia.
  6. "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(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY ORGANIZATION, NOMENCLATURE.
  7. "Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis."
    Saracco S.A., Hansson M., Scalf M., Walker J.M., Smith L.M., Vierstra R.D.
    Plant J. 59:344-358(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiUBP13_ARATH
AccessioniPrimary (citable) accession number: Q84WU2
Secondary accession number(s): Q0WVD3, Q9FU99, Q9SF08
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: June 1, 2003
Last modified: October 29, 2014
This is version 81 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