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O76075

- DFFB_HUMAN

UniProt

O76075 - DFFB_HUMAN

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Protein

DNA fragmentation factor subunit beta

Gene

DFFB

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

Functioni

Nuclease that induces DNA fragmentation and chromatin condensation during apoptosis. Degrades naked DNA and induces apoptotic morphology.

Enzyme regulationi

Inhibited by DFFA (DFF45).

GO - Molecular functioni

  1. deoxyribonuclease activity Source: RefGenome
  2. DNA binding Source: Ensembl
  3. enzyme binding Source: UniProtKB

GO - Biological processi

  1. apoptotic chromosome condensation Source: UniProtKB
  2. apoptotic DNA fragmentation Source: MGI
  3. apoptotic process Source: Reactome
  4. brain development Source: Ensembl
  5. cellular component disassembly involved in execution phase of apoptosis Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Nuclease

Keywords - Biological processi

Apoptosis

Enzyme and pathway databases

ReactomeiREACT_13462. Activation of DNA fragmentation factor.
SignaLinkiO76075.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA fragmentation factor subunit beta (EC:3.-.-.-)
Alternative name(s):
Caspase-activated deoxyribonuclease
Short name:
CAD
Short name:
Caspase-activated DNase
Caspase-activated nuclease
Short name:
CPAN
DNA fragmentation factor 40 kDa subunit
Short name:
DFF-40
Gene namesi
Name:DFFB
Synonyms:CAD, DFF2, DFF40
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 1

Organism-specific databases

HGNCiHGNC:2773. DFFB.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: UniProtKB
  2. nuclear chromatin Source: UniProtKB
  3. nucleoplasm Source: Reactome
  4. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA27255.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 338338DNA fragmentation factor subunit betaPRO_0000144713Add
BLAST

Proteomic databases

MaxQBiO76075.
PaxDbiO76075.
PRIDEiO76075.

PTM databases

PhosphoSiteiO76075.

Expressioni

Gene expression databases

BgeeiO76075.
CleanExiHS_CAD.
HS_DFFB.
ExpressionAtlasiO76075. baseline and differential.
GenevestigatoriO76075.

Organism-specific databases

HPAiCAB004328.

Interactioni

Subunit structurei

Heterodimer of DFFA and DFFB. Interacts with HIST1H1A.1 Publication

Protein-protein interaction databases

BioGridi108041. 15 interactions.
IntActiO76075. 8 interactions.
MINTiMINT-365482.
STRINGi9606.ENSP00000367454.

Structurei

Secondary structure

1
338
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi9 – 113
Beta strandi13 – 164
Helixi26 – 3611
Turni41 – 433
Beta strandi44 – 518
Beta strandi57 – 593
Beta strandi69 – 724
Beta strandi74 – 763

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IBXNMR-A1-80[»]
ProteinModelPortaliO76075.
SMRiO76075. Positions 1-326.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO76075.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini4 – 8077CIDE-NPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 CIDE-N domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiNOG68641.
GeneTreeiENSGT00390000014490.
HOGENOMiHOG000006502.
HOVERGENiHBG003828.
InParanoidiO76075.
KOiK02311.
OMAiAGQTWQG.
OrthoDBiEOG712TW8.
PhylomeDBiO76075.
TreeFamiTF102022.

Family and domain databases

InterProiIPR015311. Apoptosis_DFF40.
IPR003508. CIDE-N_dom.
[Graphical view]
PfamiPF02017. CIDE-N. 1 hit.
PF09230. DFF40. 1 hit.
[Graphical view]
PROSITEiPS51135. CIDE_N. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. Align

Isoform Alpha (identifier: O76075-1) [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
MLQKPKSVKL RALRSPRKFG VAGRSCQEVL RKGCLRFQLP ERGSRLCLYE
60 70 80 90 100
DGTELTEDYF PSVPDNAELV LLTLGQAWQG YVSDIRRFLS AFHEPQVGLI
110 120 130 140 150
QAAQQLLCDE QAPQRQRLLA DLLHNVSQNI AAETRAEDPP WFEGLESRFQ
160 170 180 190 200
SKSGYLRYSC ESRIRSYLRE VSSYPSTVGA EAQEEFLRVL GSMCQRLRSM
210 220 230 240 250
QYNGSYFDRG AKGGSRLCTP EGWFSCQGPF DMDSCLSRHS INPYSNRESR
260 270 280 290 300
ILFSTWNLDH IIEKKRTIIP TLVEAIKEQD GREVDWEYFY GLLFTSENLK
310 320 330
LVHIVCHKKT THKLNCDPSR IYKPQTRLKR KQPVRKRQ
Length:338
Mass (Da):39,110
Last modified:November 1, 1998 - v1
Checksum:i0B0F3F8D91209389
GO
Isoform Beta (identifier: O76075-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     262-338: IEKKRTIIPT...KRKQPVRKRQ → DGVLLCGPG

Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Show »
Length:270
Mass (Da):30,649
Checksum:i26AC88793BE46E7E
GO
Isoform Gamma (identifier: O76075-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     81-116: YVSDIRRFLSAFHEPQVGLIQAAQQLLCDEQAPQRQ → SVGVRARTKTRDTSSLSPGDCQALGNGGRCGQRLFL
     117-338: Missing.

Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Show »
Length:116
Mass (Da):12,800
Checksum:iF6C9A328ACBB54EE
GO
Isoform Delta (identifier: O76075-4) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     81-103: YVSDIRRFLSAFHEPQVGLIQAA → WFCHVSQDSLTLLGSSCPPALVS
     104-338: Missing.

Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Show »
Length:103
Mass (Da):11,482
Checksum:iF9BDC40AC25E4500
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti196 – 1961R → K.1 Publication
Corresponds to variant rs12738235 [ dbSNP | Ensembl ].
VAR_009305
Natural varianti277 – 2771K → R.
Corresponds to variant rs12564400 [ dbSNP | Ensembl ].
VAR_048737

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei81 – 11636YVSDI…APQRQ → SVGVRARTKTRDTSSLSPGD CQALGNGGRCGQRLFL in isoform Gamma. 1 PublicationVSP_001081Add
BLAST
Alternative sequencei81 – 10323YVSDI…LIQAA → WFCHVSQDSLTLLGSSCPPA LVS in isoform Delta. 1 PublicationVSP_001083Add
BLAST
Alternative sequencei104 – 338235Missing in isoform Delta. 1 PublicationVSP_001084Add
BLAST
Alternative sequencei117 – 338222Missing in isoform Gamma. 1 PublicationVSP_001082Add
BLAST
Alternative sequencei262 – 33877IEKKR…VRKRQ → DGVLLCGPG in isoform Beta. 1 PublicationVSP_001080Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF064019 mRNA. Translation: AAC39920.1.
AB013918 mRNA. Translation: BAA32250.1.
AF039210 mRNA. Translation: AAC39709.1.
AB028911 mRNA. Translation: BAB40447.1.
AB028912 mRNA. Translation: BAB40448.1.
AB028913 mRNA. Translation: BAB40449.1.
AK290877 mRNA. Translation: BAF83566.1.
AL691523 Genomic DNA. Translation: CAI17371.1.
BC048797 mRNA. Translation: AAH48797.1.
CCDSiCCDS52.1. [O76075-1]
RefSeqiNP_004393.1. NM_004402.3. [O76075-1]
UniGeneiHs.133089.

Genome annotation databases

EnsembliENST00000339350; ENSP00000343218; ENSG00000169598. [O76075-3]
ENST00000378209; ENSP00000367454; ENSG00000169598. [O76075-1]
ENST00000491998; ENSP00000436775; ENSG00000169598. [O76075-2]
GeneIDi1677.
KEGGihsa:1677.
UCSCiuc001alc.3. human. [O76075-1]
uc009vlo.1. human. [O76075-2]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF064019 mRNA. Translation: AAC39920.1 .
AB013918 mRNA. Translation: BAA32250.1 .
AF039210 mRNA. Translation: AAC39709.1 .
AB028911 mRNA. Translation: BAB40447.1 .
AB028912 mRNA. Translation: BAB40448.1 .
AB028913 mRNA. Translation: BAB40449.1 .
AK290877 mRNA. Translation: BAF83566.1 .
AL691523 Genomic DNA. Translation: CAI17371.1 .
BC048797 mRNA. Translation: AAH48797.1 .
CCDSi CCDS52.1. [O76075-1 ]
RefSeqi NP_004393.1. NM_004402.3. [O76075-1 ]
UniGenei Hs.133089.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1IBX NMR - A 1-80 [» ]
ProteinModelPortali O76075.
SMRi O76075. Positions 1-326.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 108041. 15 interactions.
IntActi O76075. 8 interactions.
MINTi MINT-365482.
STRINGi 9606.ENSP00000367454.

PTM databases

PhosphoSitei O76075.

Proteomic databases

MaxQBi O76075.
PaxDbi O76075.
PRIDEi O76075.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000339350 ; ENSP00000343218 ; ENSG00000169598 . [O76075-3 ]
ENST00000378209 ; ENSP00000367454 ; ENSG00000169598 . [O76075-1 ]
ENST00000491998 ; ENSP00000436775 ; ENSG00000169598 . [O76075-2 ]
GeneIDi 1677.
KEGGi hsa:1677.
UCSCi uc001alc.3. human. [O76075-1 ]
uc009vlo.1. human. [O76075-2 ]

Organism-specific databases

CTDi 1677.
GeneCardsi GC01P003797.
HGNCi HGNC:2773. DFFB.
HPAi CAB004328.
MIMi 601883. gene.
neXtProti NX_O76075.
PharmGKBi PA27255.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG68641.
GeneTreei ENSGT00390000014490.
HOGENOMi HOG000006502.
HOVERGENi HBG003828.
InParanoidi O76075.
KOi K02311.
OMAi AGQTWQG.
OrthoDBi EOG712TW8.
PhylomeDBi O76075.
TreeFami TF102022.

Enzyme and pathway databases

Reactomei REACT_13462. Activation of DNA fragmentation factor.
SignaLinki O76075.

Miscellaneous databases

EvolutionaryTracei O76075.
GeneWikii DFFB.
GenomeRNAii 1677.
NextBioi 6902.
PROi O76075.
SOURCEi Search...

Gene expression databases

Bgeei O76075.
CleanExi HS_CAD.
HS_DFFB.
ExpressionAtlasi O76075. baseline and differential.
Genevestigatori O76075.

Family and domain databases

InterProi IPR015311. Apoptosis_DFF40.
IPR003508. CIDE-N_dom.
[Graphical view ]
Pfami PF02017. CIDE-N. 1 hit.
PF09230. DFF40. 1 hit.
[Graphical view ]
PROSITEi PS51135. CIDE_N. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The 40-kDa subunit of DNA fragmentation factor induces DNA fragmentation and chromatin condensation during apoptosis."
    Liu X., Li P., Widlak P., Zou H., Luo X., Garrard W.T., Wang X.
    Proc. Natl. Acad. Sci. U.S.A. 95:8461-8466(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM ALPHA).
  2. "Molecular cloning and characterization of human caspase-activated DNase."
    Mukae N., Enari M., Sakahira H., Fukuda Y., Inazawa J., Toh H., Nagata S.
    Proc. Natl. Acad. Sci. U.S.A. 95:9123-9128(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM ALPHA).
  3. "CPAN, a human nuclease regulated by the caspase-sensitive inhibitor DFF45."
    Halenbeck R., MacDonald H., Roulston A., Chen T.T., Conroy L., Williams L.T.
    Curr. Biol. 8:537-540(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM ALPHA).
    Tissue: Pancreas.
  4. "DFF40 delta."
    Nakagawara A., Takahashi M., Takada N., Kawamoto T.
    Submitted (JUN-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS BETA; GAMMA AND DELTA).
    Tissue: Fetal brain.
  5. "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 ALPHA).
  6. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  7. "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 ALPHA).
    Tissue: Lung.
  8. Cited for: SPLICE ISOFORM(S) THAT ARE POTENTIAL NMD TARGET(S).
  9. "Histone H1 subtype preferences of DFF40 and possible nuclear localization of DFF40/45 in normal and trichostatin A-treated NB4 leukemic cells."
    Ninios Y.P., Sekeri-Pataryas K.E., Sourlingas T.G.
    Apoptosis 15:128-138(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HIST1H1A.
  10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "Structure and mutation analysis of the gene encoding DNA fragmentation factor 40 (caspase-activated nuclease), a candidate neuroblastoma tumour suppressor gene."
    Judson H., van Roy N., Strain L., Vandesompele J., Van Gele M., Speleman F., Bonthron D.T.
    Hum. Genet. 106:406-413(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT LYS-196.

Entry informationi

Entry nameiDFFB_HUMAN
AccessioniPrimary (citable) accession number: O76075
Secondary accession number(s): O60521
, Q5SR22, Q9BYI4, Q9BYI5, Q9BYI6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: November 1, 1998
Last modified: October 29, 2014
This is version 130 of the entry and version 1 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3