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Protein

Programmed cell death protein 2

Gene

PDCD2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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: UniProtKB
  3. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. activation of cysteine-type endopeptidase activity involved in apoptotic process Source: UniProtKB
  2. apoptotic process Source: ProtInc
  3. positive regulation of apoptotic process Source: UniProtKB
  4. positive regulation of hematopoietic stem cell proliferation Source: UniProtKB
  5. regulation of hematopoietic progenitor cell differentiation Source: UniProtKB
Complete GO annotation...

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: UniProtKB
  3. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

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

BgeeiQ16342.
CleanExiHS_PDCD2.
ExpressionAtlasiQ16342. baseline and differential.
GenevestigatoriQ16342.

Organism-specific databases

HPAiHPA026713.

Interactioni

Binary interactionsi

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

Protein-protein interaction databases

BioGridi111161. 10 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.
GeneTreeiENSGT00530000063570.
HOGENOMiHOG000237274.
HOVERGENiHBG053535.
InParanoidiQ16342.
KOiK14801.
OMAiVCGCLAP.
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

        10         20         30         40         50
MAAAGARPVE LGFAESAPAW RLRSEQFPSK VGGRPAWLGA AGLPGPQALA
60 70 80 90 100
CELCGRPLSF LLQVYAPLPG RPDAFHRCIF LFCCREQPCC AGLRVFRNQL
110 120 130 140 150
PRKNDFYSYE PPSENPPPET GESVCLQLKS GAHLCRVCGC LGPKTCSRCH
160 170 180 190 200
KAYYCSKEHQ TLDWRLGHKQ ACAQPDHLDH IIPDHNFLFP EFEIVIETED
210 220 230 240 250
EIMPEVVEKE DYSEIIGSMG EALEEELDSM AKHESREDKI FQKFKTQIAL
260 270 280 290 300
EPEQILRYGR GIAPIWISGE NIPQEKDIPD CPCGAKRILE FQVMPQLLNY
310 320 330 340
LKADRLGKSI DWGILAVFTC AESCSLGTGY TEEFVWKQDV TDTP
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:
EMBLi
GenBanki
DDBJi
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. [Q16342-5]
NP_002589.2. NM_002598.3. [Q16342-1]
NP_659005.1. NM_144781.2. [Q16342-4]
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:
EMBLi
GenBanki
DDBJi
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. [Q16342-5]
NP_002589.2. NM_002598.3. [Q16342-1]
NP_659005.1. NM_144781.2. [Q16342-4]
UniGeneiHs.367900.

3D structure databases

ProteinModelPortaliQ16342.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111161. 10 interactions.
DIPiDIP-27594N.
IntActiQ16342. 8 interactions.
MINTiMINT-1133310.
STRINGi9606.ENSP00000167218.

PTM databases

PhosphoSiteiQ16342.

Polymorphism databases

DMDMi28202261.

Proteomic databases

MaxQBiQ16342.
PaxDbiQ16342.
PRIDEiQ16342.

Protocols and materials databases

DNASUi5134.
Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi5134.
GeneCardsiGC06M170884.
HGNCiHGNC:8762. PDCD2.
HPAiHPA026713.
MIMi600866. gene.
neXtProtiNX_Q16342.
PharmGKBiPA33112.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG238796.
GeneTreeiENSGT00530000063570.
HOGENOMiHOG000237274.
HOVERGENiHBG053535.
InParanoidiQ16342.
KOiK14801.
OMAiVCGCLAP.
OrthoDBiEOG722J96.
PhylomeDBiQ16342.
TreeFamiTF313722.

Miscellaneous databases

GeneWikiiPDCD2.
GenomeRNAii5134.
NextBioi19796.
PROiQ16342.
SOURCEiSearch...

Gene expression databases

BgeeiQ16342.
CleanExiHS_PDCD2.
ExpressionAtlasiQ16342. baseline and differential.
GenevestigatoriQ16342.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: February 4, 2015
This is version 136 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

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.