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Q16342

- PDCD2_HUMAN

UniProt

Q16342 - PDCD2_HUMAN

Protein

Programmed cell death protein 2

Gene

PDCD2

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
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    • History
      Entry version 133 (01 Oct 2014)
      Sequence version 2 (01 Feb 2003)
      Previous versions | rss
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    Functioni

    May be a DNA-binding protein with a regulatory function. May play an important role in cell death and/or in regulation of cell proliferation.

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri135 – 17238MYND-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. enzyme binding Source: UniProt
    3. metal ion binding Source: UniProtKB-KW
    4. protein binding Source: IntAct

    GO - Biological processi

    1. apoptotic process Source: ProtInc

    Keywords - Biological processi

    Apoptosis

    Keywords - Ligandi

    DNA-binding, Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Programmed cell death protein 2
    Alternative name(s):
    Zinc finger MYND domain-containing protein 7
    Zinc finger protein Rp-8
    Gene namesi
    Name:PDCD2
    Synonyms:RP8, ZMYND7
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 6

    Organism-specific databases

    HGNCiHGNC:8762. PDCD2.

    Subcellular locationi

    Nucleus Curated

    GO - Cellular componenti

    1. cytoplasm Source: InterPro
    2. extracellular vesicular exosome Source: UniProt
    3. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA33112.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 344344Programmed cell death protein 2PRO_0000218304Add
    BLAST

    Post-translational modificationi

    Ubiquitinated by PARK2, promoting proteasomal degradation.1 Publication

    Keywords - PTMi

    Ubl conjugation

    Proteomic databases

    MaxQBiQ16342.
    PaxDbiQ16342.
    PRIDEiQ16342.

    PTM databases

    PhosphoSiteiQ16342.

    Expressioni

    Tissue specificityi

    Ubiquitous.

    Gene expression databases

    ArrayExpressiQ16342.
    BgeeiQ16342.
    CleanExiHS_PDCD2.
    GenevestigatoriQ16342.

    Organism-specific databases

    HPAiHPA026713.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    PARK2O602605EBI-359462,EBI-716346

    Protein-protein interaction databases

    BioGridi111161. 8 interactions.
    DIPiDIP-27594N.
    IntActiQ16342. 8 interactions.
    MINTiMINT-1133310.
    STRINGi9606.ENSP00000167218.

    Structurei

    3D structure databases

    ProteinModelPortaliQ16342.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Contains 1 MYND-type zinc finger.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri135 – 17238MYND-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiNOG238796.
    HOGENOMiHOG000237274.
    HOVERGENiHBG053535.
    InParanoidiQ16342.
    KOiK14801.
    OMAiRILEFQV.
    OrthoDBiEOG722J96.
    PhylomeDBiQ16342.
    TreeFamiTF313722.

    Family and domain databases

    InterProiIPR007320. PDCD2_C.
    IPR002893. Znf_MYND.
    [Graphical view]
    PfamiPF04194. PDCD2_C. 1 hit.
    PF01753. zf-MYND. 1 hit.
    [Graphical view]
    PROSITEiPS01360. ZF_MYND_1. 1 hit.
    PS50865. ZF_MYND_2. 1 hit.
    [Graphical view]

    Sequences (5)i

    Sequence statusi: Complete.

    This entry describes 5 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q16342-1) [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

    MAAAGARPVE LGFAESAPAW RLRSEQFPSK VGGRPAWLGA AGLPGPQALA    50
    CELCGRPLSF LLQVYAPLPG RPDAFHRCIF LFCCREQPCC AGLRVFRNQL 100
    PRKNDFYSYE PPSENPPPET GESVCLQLKS GAHLCRVCGC LGPKTCSRCH 150
    KAYYCSKEHQ TLDWRLGHKQ ACAQPDHLDH IIPDHNFLFP EFEIVIETED 200
    EIMPEVVEKE DYSEIIGSMG EALEEELDSM AKHESREDKI FQKFKTQIAL 250
    EPEQILRYGR GIAPIWISGE NIPQEKDIPD CPCGAKRILE FQVMPQLLNY 300
    LKADRLGKSI DWGILAVFTC AESCSLGTGY TEEFVWKQDV TDTP 344
    Length:344
    Mass (Da):38,592
    Last modified:February 1, 2003 - v2
    Checksum:iF3E7BA2C9FBAFD0E
    GO
    Isoform 2 (identifier: Q16342-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         31-63: Missing.
         221-344: EALEEELDSM...VWKQDVTDTP → KQFQDFIH

    Show »
    Length:195
    Mass (Da):22,230
    Checksum:i2A29B0D0A276CB6D
    GO
    Isoform 3 (identifier: Q16342-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         31-63: Missing.

    Show »
    Length:311
    Mass (Da):35,290
    Checksum:i2690DDD960B82B1C
    GO
    Isoform 4 (identifier: Q16342-4) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         221-228: EALEEELD → KQFQDFIH
         229-344: Missing.

    Note: No experimental confirmation available. Gene prediction based on partial EST data.

    Show »
    Length:228
    Mass (Da):25,532
    Checksum:i7BE1A0F6BE9306FD
    GO
    Isoform 5 (identifier: Q16342-5) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         31-63: Missing.
         221-221: E → I
         222-344: Missing.

    Note: No experimental confirmation available. Gene prediction based on partial EST data.

    Show »
    Length:188
    Mass (Da):21,299
    Checksum:iDE1D2BC8F2529930
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti226 – 2261E → G in AAB34865. (PubMed:7606924)Curated
    Sequence conflicti317 – 3171V → A in AAB34865. (PubMed:7606924)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei31 – 6333Missing in isoform 2, isoform 3 and isoform 5. 2 PublicationsVSP_042828Add
    BLAST
    Alternative sequencei221 – 344124EALEE…VTDTP → KQFQDFIH in isoform 2. 2 PublicationsVSP_042829Add
    BLAST
    Alternative sequencei221 – 2288EALEEELD → KQFQDFIH in isoform 4. CuratedVSP_055159
    Alternative sequencei221 – 2211E → I in isoform 5. CuratedVSP_055160
    Alternative sequencei222 – 344123Missing in isoform 5. CuratedVSP_055161Add
    BLAST
    Alternative sequencei229 – 344116Missing in isoform 4. CuratedVSP_055162Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    S78085 mRNA. Translation: AAB34865.1.
    AY948416 mRNA. Translation: AAX51225.1.
    AY948417 mRNA. Translation: AAX51226.1.
    AK297343 mRNA. Translation: BAG59795.1.
    AL031259 Genomic DNA. Translation: CAA20285.1.
    BC008378 mRNA. Translation: AAH08378.1.
    CCDSiCCDS47521.1. [Q16342-4]
    CCDS5316.1. [Q16342-1]
    CCDS56460.1. [Q16342-2]
    CCDS56461.1. [Q16342-3]
    CCDS56462.1. [Q16342-5]
    PIRiI52969.
    RefSeqiNP_001186391.1. NM_001199462.1. [Q16342-3]
    NP_001186392.1. NM_001199463.1. [Q16342-2]
    NP_001186393.1. NM_001199464.1.
    NP_002589.2. NM_002598.3. [Q16342-1]
    NP_659005.1. NM_144781.2.
    UniGeneiHs.367900.

    Genome annotation databases

    EnsembliENST00000392090; ENSP00000375940; ENSG00000071994. [Q16342-3]
    ENST00000443345; ENSP00000397272; ENSG00000071994. [Q16342-2]
    ENST00000453163; ENSP00000402524; ENSG00000071994. [Q16342-4]
    ENST00000537445; ENSP00000440572; ENSG00000071994. [Q16342-5]
    ENST00000541970; ENSP00000439467; ENSG00000071994. [Q16342-1]
    GeneIDi5134.
    KEGGihsa:5134.
    UCSCiuc003qxv.3. human. [Q16342-3]
    uc003qxw.3. human. [Q16342-1]
    uc003qxy.3. human. [Q16342-2]

    Polymorphism databases

    DMDMi28202261.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    S78085 mRNA. Translation: AAB34865.1 .
    AY948416 mRNA. Translation: AAX51225.1 .
    AY948417 mRNA. Translation: AAX51226.1 .
    AK297343 mRNA. Translation: BAG59795.1 .
    AL031259 Genomic DNA. Translation: CAA20285.1 .
    BC008378 mRNA. Translation: AAH08378.1 .
    CCDSi CCDS47521.1. [Q16342-4 ]
    CCDS5316.1. [Q16342-1 ]
    CCDS56460.1. [Q16342-2 ]
    CCDS56461.1. [Q16342-3 ]
    CCDS56462.1. [Q16342-5 ]
    PIRi I52969.
    RefSeqi NP_001186391.1. NM_001199462.1. [Q16342-3 ]
    NP_001186392.1. NM_001199463.1. [Q16342-2 ]
    NP_001186393.1. NM_001199464.1.
    NP_002589.2. NM_002598.3. [Q16342-1 ]
    NP_659005.1. NM_144781.2.
    UniGenei Hs.367900.

    3D structure databases

    ProteinModelPortali Q16342.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 111161. 8 interactions.
    DIPi DIP-27594N.
    IntActi Q16342. 8 interactions.
    MINTi MINT-1133310.
    STRINGi 9606.ENSP00000167218.

    PTM databases

    PhosphoSitei Q16342.

    Polymorphism databases

    DMDMi 28202261.

    Proteomic databases

    MaxQBi Q16342.
    PaxDbi Q16342.
    PRIDEi Q16342.

    Protocols and materials databases

    DNASUi 5134.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000392090 ; ENSP00000375940 ; ENSG00000071994 . [Q16342-3 ]
    ENST00000443345 ; ENSP00000397272 ; ENSG00000071994 . [Q16342-2 ]
    ENST00000453163 ; ENSP00000402524 ; ENSG00000071994 . [Q16342-4 ]
    ENST00000537445 ; ENSP00000440572 ; ENSG00000071994 . [Q16342-5 ]
    ENST00000541970 ; ENSP00000439467 ; ENSG00000071994 . [Q16342-1 ]
    GeneIDi 5134.
    KEGGi hsa:5134.
    UCSCi uc003qxv.3. human. [Q16342-3 ]
    uc003qxw.3. human. [Q16342-1 ]
    uc003qxy.3. human. [Q16342-2 ]

    Organism-specific databases

    CTDi 5134.
    GeneCardsi GC06M170884.
    HGNCi HGNC:8762. PDCD2.
    HPAi HPA026713.
    MIMi 600866. gene.
    neXtProti NX_Q16342.
    PharmGKBi PA33112.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG238796.
    HOGENOMi HOG000237274.
    HOVERGENi HBG053535.
    InParanoidi Q16342.
    KOi K14801.
    OMAi RILEFQV.
    OrthoDBi EOG722J96.
    PhylomeDBi Q16342.
    TreeFami TF313722.

    Miscellaneous databases

    GeneWikii PDCD2.
    GenomeRNAii 5134.
    NextBioi 19796.
    PROi Q16342.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q16342.
    Bgeei Q16342.
    CleanExi HS_PDCD2.
    Genevestigatori Q16342.

    Family and domain databases

    InterProi IPR007320. PDCD2_C.
    IPR002893. Znf_MYND.
    [Graphical view ]
    Pfami PF04194. PDCD2_C. 1 hit.
    PF01753. zf-MYND. 1 hit.
    [Graphical view ]
    PROSITEi PS01360. ZF_MYND_1. 1 hit.
    PS50865. ZF_MYND_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Isolation and mapping of a human gene (PDCD2) that is highly homologous to Rp8, a rat gene associated with programmed cell death."
      Kawakami T., Furukawa Y., Sudo K., Saito H., Takami S., Takahashi E., Nakamura Y.
      Cytogenet. Cell Genet. 71:41-43(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
      Tissue: Fetal lung.
    2. "Cloning of cDNAs with PDCD_2 domain and their expression during apoptosis of HEK293T cells."
      Chen Q., Qian K.X.
      Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 2 AND 3).
    3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Tissue: Brain.
    4. "The DNA sequence and analysis of human chromosome 6."
      Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
      , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
      Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Lung.
    6. "Programmed cell death-2 isoform1 is ubiquitinated by parkin and increased in the substantia nigra of patients with autosomal recessive Parkinson's disease."
      Fukae J., Sato S., Shiba K., Sato K., Mori H., Sharp P.A., Mizuno Y., Hattori N.
      FEBS Lett. 583:521-525(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: UBIQUITINATION BY PARK2.
    7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiPDCD2_HUMAN
    AccessioniPrimary (citable) accession number: Q16342
    Secondary accession number(s): E9PCU7
    , F5GYS7, Q58HM9, Q58HN0, Q9UH12
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 2000
    Last sequence update: February 1, 2003
    Last modified: October 1, 2014
    This is version 133 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome 6
      Human chromosome 6: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3