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Q8VX13

- PDI13_ARATH

UniProt

Q8VX13 - PDI13_ARATH

Protein

Protein disulfide isomerase-like 1-3

Gene

PDIL1-3

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 105 (01 Oct 2014)
      Sequence version 1 (01 Mar 2002)
      Previous versions | rss
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    Functioni

    Acts as a protein-folding catalyst that interacts with nascent polypeptides to catalyze the formation, isomerization, and reduction or oxidation of disulfide bonds.By similarity

    Catalytic activityi

    Catalyzes the rearrangement of -S-S- bonds in proteins.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei128 – 1281NucleophileBy similarity
    Active sitei131 – 1311NucleophileBy similarity
    Sitei190 – 1901Lowers pKa of C-terminal Cys of first active siteBy similarity
    Active sitei467 – 4671NucleophileBy similarity
    Sitei468 – 4681Contributes to redox potential valueBy similarity
    Sitei469 – 4691Contributes to redox potential valueBy similarity
    Active sitei470 – 4701NucleophileBy similarity
    Sitei532 – 5321Lowers pKa of C-terminal Cys of second active siteBy similarity

    GO - Molecular functioni

    1. protein disulfide isomerase activity Source: TAIR

    GO - Biological processi

    1. cell redox homeostasis Source: InterPro
    2. response to endoplasmic reticulum stress Source: TAIR

    Keywords - Molecular functioni

    Isomerase

    Enzyme and pathway databases

    BioCyciARA:AT3G54960-MONOMER.
    ARA:GQT-1367-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protein disulfide isomerase-like 1-3 (EC:5.3.4.1)
    Short name:
    AtPDIL1-3
    Alternative name(s):
    Protein disulfide isomerase 1
    Short name:
    AtPDI1
    Protein disulfide isomerase-like 2-1
    Short name:
    AtPDIL2-1
    Gene namesi
    Name:PDIL1-3
    Synonyms:PDI1, PDI72, PDIL2-1
    Ordered Locus Names:At3g54960
    ORF Names:F28P10.60, T15C9.4
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 3

    Organism-specific databases

    TAIRiAT3G54960.

    Subcellular locationi

    GO - Cellular componenti

    1. chloroplast Source: TAIR
    2. endoplasmic reticulum Source: TAIR
    3. endoplasmic reticulum lumen Source: UniProtKB-SubCell
    4. vacuolar membrane Source: TAIR

    Keywords - Cellular componenti

    Endoplasmic reticulum

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2525Sequence AnalysisAdd
    BLAST
    Chaini26 – 579554Protein disulfide isomerase-like 1-3PRO_5000065917Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi27 – 271N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi108 – 1081N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi115 – 1151N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi128 ↔ 131Redox-activePROSITE-ProRule annotation
    Glycosylationi209 – 2091N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi293 – 2931N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi313 – 3131N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi338 – 3381N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi467 ↔ 470Redox-activePROSITE-ProRule annotation
    Glycosylationi520 – 5201N-linked (GlcNAc...)Sequence Analysis

    Keywords - PTMi

    Disulfide bond, Glycoprotein

    Proteomic databases

    PaxDbiQ8VX13.
    PRIDEiQ8VX13.

    Expressioni

    Tissue specificityi

    Widely expressed.1 Publication

    Inductioni

    By chemically-induced ER stress response.1 Publication

    Gene expression databases

    GenevestigatoriQ8VX13.

    Interactioni

    Protein-protein interaction databases

    BioGridi9977. 1 interaction.
    IntActiQ8VX13. 1 interaction.
    STRINGi3702.AT3G54960.1-P.

    Structurei

    3D structure databases

    ProteinModelPortaliQ8VX13.
    SMRiQ8VX13. Positions 95-546.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini81 – 204124Thioredoxin 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini416 – 546131Thioredoxin 2PROSITE-ProRule annotationAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi576 – 5794Prevents secretion from ERPROSITE-ProRule annotation

    Sequence similaritiesi

    Belongs to the protein disulfide isomerase family.Curated
    Contains 2 thioredoxin domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Redox-active center, Repeat, Signal

    Phylogenomic databases

    eggNOGiCOG0526.
    HOGENOMiHOG000162459.
    InParanoidiQ8VX13.
    KOiK09580.
    OMAiANESEKH.
    PhylomeDBiQ8VX13.

    Family and domain databases

    Gene3Di3.40.30.10. 4 hits.
    InterProiIPR005792. Prot_disulphide_isomerase.
    IPR012336. Thioredoxin-like_fold.
    IPR017937. Thioredoxin_CS.
    IPR013766. Thioredoxin_domain.
    [Graphical view]
    PfamiPF00085. Thioredoxin. 2 hits.
    [Graphical view]
    SUPFAMiSSF52833. SSF52833. 4 hits.
    TIGRFAMsiTIGR01130. ER_PDI_fam. 1 hit.
    PROSITEiPS00014. ER_TARGET. 1 hit.
    PS00194. THIOREDOXIN_1. 2 hits.
    PS51352. THIOREDOXIN_2. 2 hits.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q8VX13-1) [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

    MASSSTSISL LLFVSFILLL VNSRAENASS GSDLDEELAF LAAEESKEQS    50
    HGGGSYHEEE HDHQHRDFEN YDDLEQGGGE FHHGDHGYEE EPLPPVDEKD 100
    VAVLTKDNFT EFVGNNSFAM VEFYAPWCGA CQALTPEYAA AATELKGLAA 150
    LAKIDATEEG DLAQKYEIQG FPTVFLFVDG EMRKTYEGER TKDGIVTWLK 200
    KKASPSIHNI TTKEEAERVL SAEPKLVFGF LNSLVGSESE ELAAASRLED 250
    DLSFYQTASP DIAKLFEIET QVKRPALVLL KKEEEKLARF DGNFTKTAIA 300
    EFVSANKVPL VINFTREGAS LIFESSVKNQ LILFAKANES EKHLPTLREV 350
    AKSFKGKFVF VYVQMDNEDY GEAVSGFFGV TGAAPKVLVY TGNEDMRKFI 400
    LDGELTVNNI KTLAEDFLAD KLKPFYKSDP LPENNDGDVK VIVGNNFDEI 450
    VLDESKDVLL EIYAPWCGHC QSFEPIYNKL GKYLKGIDSL VVAKMDGTSN 500
    EHPRAKADGF PTILFFPGGN KSFDPIAVDV DRTVVELYKF LKKHASIPFK 550
    LEKPATPEPV ISTMKSDEKI EGDSSKDEL 579
    Length:579
    Mass (Da):64,212
    Last modified:March 1, 2002 - v1
    Checksum:i0DF50E500B24B829
    GO
    Isoform 2 (identifier: Q8VX13-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         507-518: ADGFPTILFFPG → VIKKKELRKSFW
         519-579: Missing.

    Note: No experimental confirmation available.

    Show »
    Length:518
    Mass (Da):57,691
    Checksum:iB3AA1BB3BAFE49FF
    GO

    Sequence cautioni

    The sequence CAB41088.1 differs from that shown. Reason: Erroneous gene model prediction.

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei507 – 51812ADGFP…LFFPG → VIKKKELRKSFW in isoform 2. 1 PublicationVSP_039979Add
    BLAST
    Alternative sequencei519 – 57961Missing in isoform 2. 1 PublicationVSP_039980Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK318844 mRNA. Translation: BAH56959.1.
    AJ271376 mRNA. Translation: CAC81067.1.
    AL049655 Genomic DNA. Translation: CAB41088.1. Sequence problems.
    AL132970 Genomic DNA. No translation available.
    CP002686 Genomic DNA. Translation: AEE79318.1.
    CP002686 Genomic DNA. Translation: AEE79319.1.
    AY093115 mRNA. Translation: AAM13114.1.
    BT000172 mRNA. Translation: AAN15491.1.
    PIRiT06724.
    RefSeqiNP_001118842.1. NM_001125370.1. [Q8VX13-2]
    NP_191056.2. NM_115353.4. [Q8VX13-1]
    UniGeneiAt.22358.

    Genome annotation databases

    EnsemblPlantsiAT3G54960.1; AT3G54960.1; AT3G54960. [Q8VX13-1]
    GeneIDi824661.
    KEGGiath:AT3G54960.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK318844 mRNA. Translation: BAH56959.1 .
    AJ271376 mRNA. Translation: CAC81067.1 .
    AL049655 Genomic DNA. Translation: CAB41088.1 . Sequence problems.
    AL132970 Genomic DNA. No translation available.
    CP002686 Genomic DNA. Translation: AEE79318.1 .
    CP002686 Genomic DNA. Translation: AEE79319.1 .
    AY093115 mRNA. Translation: AAM13114.1 .
    BT000172 mRNA. Translation: AAN15491.1 .
    PIRi T06724.
    RefSeqi NP_001118842.1. NM_001125370.1. [Q8VX13-2 ]
    NP_191056.2. NM_115353.4. [Q8VX13-1 ]
    UniGenei At.22358.

    3D structure databases

    ProteinModelPortali Q8VX13.
    SMRi Q8VX13. Positions 95-546.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 9977. 1 interaction.
    IntActi Q8VX13. 1 interaction.
    STRINGi 3702.AT3G54960.1-P.

    Proteomic databases

    PaxDbi Q8VX13.
    PRIDEi Q8VX13.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT3G54960.1 ; AT3G54960.1 ; AT3G54960 . [Q8VX13-1 ]
    GeneIDi 824661.
    KEGGi ath:AT3G54960.

    Organism-specific databases

    TAIRi AT3G54960.

    Phylogenomic databases

    eggNOGi COG0526.
    HOGENOMi HOG000162459.
    InParanoidi Q8VX13.
    KOi K09580.
    OMAi ANESEKH.
    PhylomeDBi Q8VX13.

    Enzyme and pathway databases

    BioCyci ARA:AT3G54960-MONOMER.
    ARA:GQT-1367-MONOMER.

    Gene expression databases

    Genevestigatori Q8VX13.

    Family and domain databases

    Gene3Di 3.40.30.10. 4 hits.
    InterProi IPR005792. Prot_disulphide_isomerase.
    IPR012336. Thioredoxin-like_fold.
    IPR017937. Thioredoxin_CS.
    IPR013766. Thioredoxin_domain.
    [Graphical view ]
    Pfami PF00085. Thioredoxin. 2 hits.
    [Graphical view ]
    SUPFAMi SSF52833. SSF52833. 4 hits.
    TIGRFAMsi TIGR01130. ER_PDI_fam. 1 hit.
    PROSITEi PS00014. ER_TARGET. 1 hit.
    PS00194. THIOREDOXIN_1. 2 hits.
    PS51352. THIOREDOXIN_2. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Arabidopsis thaliana mRNA for ERp72."
      Mahon P.
      Thesis (2000), Cambridge University, United Kingdom
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    2. "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.
    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] (ISOFORM 1).
      Strain: cv. Columbia.
    5. "Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs."
      Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K.
      DNA Res. 16:155-164(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Strain: cv. Columbia.
    6. "Phylogenetic analyses identify 10 classes of the protein disulfide isomerase family in plants, including single-domain protein disulfide isomerase-related proteins."
      Houston N.L., Fan C., Xiang J.Q., Schulze J.M., Jung R., Boston R.S.
      Plant Physiol. 137:762-778(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENE FAMILY, NOMENCLATURE.
    7. "Endoplasmic reticulum stress activates the expression of a sub-group of protein disulfide isomerase genes and AtbZIP60 modulates the response in Arabidopsis thaliana."
      Lu D.-P., Christopher D.A.
      Mol. Genet. Genomics 280:199-210(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY, INDUCTION.
    8. "The protein disulfide isomerase gene family in bread wheat (T. aestivum L.)."
      d'Aloisio E., Paolacci A.R., Dhanapal A.P., Tanzarella O.A., Porceddu E., Ciaffi M.
      BMC Plant Biol. 10:101-101(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENE FAMILY, NOMENCLATURE.

    Entry informationi

    Entry nameiPDI13_ARATH
    AccessioniPrimary (citable) accession number: Q8VX13
    Secondary accession number(s): B3H5N9, Q9SV44
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 2, 2010
    Last sequence update: March 1, 2002
    Last modified: October 1, 2014
    This is version 105 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. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3