Summary: DNA Fragmentation factor 45kDa, C terminal domain

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Wikipedia: DFFA
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DFFA Edit Wikipedia article

DNA fragmentation factor, 45kDa, alpha polypeptide

PDB rendering based on 1iyr.

Available structures

PDB

Ortholog search: PDBe, RCSB

List of PDB id codes
1IBX, 1IYR, 1KOY

Identifiers

Symbols

DFFA; DFF-45; DFF1; ICAD

External IDs

OMIM: 601882 MGI: 1196227 HomoloGene: 3240 GeneCards: DFFA Gene

Gene Ontology
Molecular function	• deoxyribonuclease activity
Cellular component	• nuclear chromatin • nucleus • nucleoplasm • cytosol
Biological process	• apoptotic DNA fragmentation • apoptotic DNA fragmentation • apoptotic process • induction of apoptosis • cellular component disassembly involved in apoptotic process • intracellular signal transduction • negative regulation of apoptotic process
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 1:
10.52 – 10.53 Mb

Chr 4:
149.1 – 149.12 Mb

PubMed search

[1]

[2]

DNA Fragmentation factor 45kDa, C terminal domain

nmr structure of dff-c domain

Identifiers

Symbol

DFF-C

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

DNA fragmentation factor subunit alpha (DFFA), also known as Inhibitor of caspase-activated DNase (ICAD), is a protein that in humans is encoded by the DFFA gene.^[1]^[2]^[3]

Apoptosis is a cell death process that removes toxic and/or useless cells during mammalian development. The apoptotic process is accompanied by shrinkage and fragmentation of the cells and nuclei and degradation of the chromosomal DNA into nucleosomal units. DNA fragmentation factor (DFF) is a heterodimeric protein of 40-kD (DFFB) and 45-kD (DFFA) subunits. DFFA is the substrate for caspase-3 and triggers DNA fragmentation during apoptosis. DFF becomes activated when DFFA is cleaved by caspase-3. The cleaved fragments of DFFA dissociate from DFFB, the active component of DFF. DFFB has been found to trigger both DNA fragmentation and chromatin condensation during apoptosis. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.^[3]

The C-terminal domain of DFFA (DFF-C) consists of four alpha-helices, which are folded in a helix-packing arrangement, with alpha-2 and alpha-3 packing against a long C-terminal helix (alpha-4). The main function of this domain is the inhibition of DFFB by binding to its C-terminal catalytic domain through ionic interactions, thereby inhibiting the fragmentation of DNA in the apoptotic process. In addition to blocking the DNase activity of DFFB, the C-terminal region of DFFA is also important for the DFFB-specific folding chaperone activity, as demonstrated by the ability of DFFA to refold DFFB.^[4]

[edit] Interactions

DFFA has been shown to interact with DFFB.^[5]^[6]

[edit] References

^ Leek JP, Carr IM, Bell SM, Markham AF, Lench NJ (Jun 1998). "Assignment of the DNA fragmentation factor gene (DFFA) to human chromosome bands 1p36.3→p36.2 by in situ hybridization". Cytogenet Cell Genet 79 (3–4): 212–3. doi:10.1159/000134725. PMID 9605855.
^ Liu X, Zou H, Slaughter C, Wang X (May 1997). "DFF, a heterodimeric protein that functions downstream of caspase-3 to trigger DNA fragmentation during apoptosis". Cell 89 (2): 175–84. doi:10.1016/S0092-8674(00)80197-X. PMID 9108473.
^ ^a ^b "Entrez Gene: DFFA DNA fragmentation factor, 45kDa, alpha polypeptide". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=1676.
^ Fukushima K, Kikuchi J, Koshiba S, Kigawa T, Kuroda Y, Yokoyama S (August 2002). "Solution structure of the DFF-C domain of DFF45/ICAD. A structural basis for the regulation of apoptotic DNA fragmentation". J. Mol. Biol. 321 (2): 317–27. doi:10.1016/S0022-2836(02)00588-0. PMID 12144788.
^ Ewing, Rob M; Chu Peter, Elisma Fred, Li Hongyan, Taylor Paul, Climie Shane, McBroom-Cerajewski Linda, Robinson Mark D, O'Connor Liam, Li Michael, Taylor Rod, Dharsee Moyez, Ho Yuen, Heilbut Adrian, Moore Lynda, Zhang Shudong, Ornatsky Olga, Bukhman Yury V, Ethier Martin, Sheng Yinglun, Vasilescu Julian, Abu-Farha Mohamed, Lambert Jean-Philippe, Duewel Henry S, Stewart Ian I, Kuehl Bonnie, Hogue Kelly, Colwill Karen, Gladwish Katharine, Muskat Brenda, Kinach Robert, Adams Sally-Lin, Moran Michael F, Morin Gregg B, Topaloglou Thodoros, Figeys Daniel (2007). "Large-scale mapping of human protein–protein interactions by mass spectrometry". Mol. Syst. Biol. (England) 3 (1): 89. doi:10.1038/msb4100134. PMC 1847948. PMID 17353931. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1847948.
^ McCarty, J S; Toh S Y, Li P (Oct. 1999). "Study of DFF45 in its role of chaperone and inhibitor: two independent inhibitory domains of DFF40 nuclease activity". Biochem. Biophys. Res. Commun. (UNITED STATES) 264 (1): 176–80. doi:10.1006/bbrc.1999.1497. ISSN 0006-291X. PMID 10527860.

[edit] Further reading

Nakanuma Y, Tsuneyama K, Sasaki M, Harada K (2000). "Destruction of bile ducts in primary biliary cirrhosis". Baillière's best practice & research. Clinical gastroenterology 14 (4): 549–70. doi:10.1053/bega.2000.0103. PMID 10976014.
Maruyama K, Sugano S (1994). "Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides". Gene 138 (1–2): 171–4. doi:10.1016/0378-1119(94)90802-8. PMID 8125298.
Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, et al. (1997). "Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library". Gene 200 (1–2): 149–56. doi:10.1016/S0378-1119(97)00411-3. PMID 9373149.
Enari M, Sakahira H, Yokoyama H, et al. (1998). "A caspase-activated DNase that degrades DNA during apoptosis, and its inhibitor ICAD". Nature 391 (6662): 43–50. doi:10.1038/34112. PMID 9422506.
Liu X, Zou H, Widlak P, et al. (1999). "Activation of the apoptotic endonuclease DFF40 (caspase-activated DNase or nuclease). Oligomerization and direct interaction with histone H1". J. Biol. Chem. 274 (20): 13836–40. doi:10.1074/jbc.274.20.13836. PMID 10318789.
Gu J, Dong RP, Zhang C, et al. (1999). "Functional interaction of DFF35 and DFF45 with caspase-activated DNA fragmentation nuclease DFF40". J. Biol. Chem. 274 (30): 20759–62. doi:10.1074/jbc.274.30.20759. PMID 10409614.
Oh JJ, Grosshans DR, Wong SG, Slamon DJ (1999). "Identification of differentially expressed genes associated with HER-2/neu overexpression in human breast cancer cells". Nucleic Acids Res. 27 (20): 4008–17. doi:10.1093/nar/27.20.4008. PMC 148668. PMID 10497265. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=148668.
McCarty JS, Toh SY, Li P (1999). "Study of DFF45 in its role of chaperone and inhibitor: two independent inhibitory domains of DFF40 nuclease activity". Biochem. Biophys. Res. Commun. 264 (1): 176–80. doi:10.1006/bbrc.1999.1497. PMID 10527860.
McCarty JS, Toh SY, Li P (1999). "Multiple domains of DFF45 bind synergistically to DFF40: roles of caspase cleavage and sequestration of activator domain of DFF40". Biochem. Biophys. Res. Commun. 264 (1): 181–5. doi:10.1006/bbrc.1999.1498. PMID 10527861.
Lugovskoy AA, Zhou P, Chou JJ, et al. (2000). "Solution structure of the CIDE-N domain of CIDE-B and a model for CIDE-N/CIDE-N interactions in the DNA fragmentation pathway of apoptosis". Cell 99 (7): 747–55. doi:10.1016/S0092-8674(00)81672-4. PMID 10619428.
Otomo T, Sakahira H, Uegaki K, et al. (2000). "Structure of the heterodimeric complex between CAD domains of CAD and ICAD". Nat. Struct. Biol. 7 (8): 658–62. doi:10.1038/77957. PMID 10932250.
Xerri L, Palmerini F, Devilard E, et al. (2000). "Frequent nuclear localization of ICAD and cytoplasmic co-expression of caspase-8 and caspase-3 in human lymphomas". J. Pathol. 192 (2): 194–202. doi:10.1002/1096-9896(2000)9999:9999<::AID-PATH685>3.0.CO;2-M. PMID 11004695.
Zhou P, Lugovskoy AA, McCarty JS, et al. (2001). "Solution structure of DFF40 and DFF45 N-terminal domain complex and mutual chaperone activity of DFF40 and DFF45". Proc. Natl. Acad. Sci. U.S.A. 98 (11): 6051–5. doi:10.1073/pnas.111145098. PMC 33420. PMID 11371636. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=33420.
Sharif-Askari E, Alam A, Rhéaume E, et al. (2001). "Direct cleavage of the human DNA fragmentation factor-45 by granzyme B induces caspase-activated DNase release and DNA fragmentation". EMBO J. 20 (12): 3101–13. doi:10.1093/emboj/20.12.3101. PMC 150191. PMID 11406587. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=150191.
Tsukada T, Watanabe M, Yamashima T (2002). "Implications of CAD and DNase II in ischemic neuronal necrosis specific for the primate hippocampus". J. Neurochem. 79 (6): 1196–206. doi:10.1046/j.1471-4159.2001.00679.x. PMID 11752060.
Abel F, Sjöberg RM, Ejeskär K, et al. (2002). "Analyses of apoptotic regulators CASP9 and DFFA at 1P36.2, reveal rare allele variants in human neuroblastoma tumours". Br. J. Cancer 86 (4): 596–604. doi:10.1038/sj.bjc.6600111. PMC 2375272. PMID 11870543. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2375272.
Charrier L, Jarry A, Toquet C, et al. (2002). "Growth phase-dependent expression of ICAD-L/DFF45 modulates the pattern of apoptosis in human colonic cancer cells". Cancer Res. 62 (7): 2169–74. PMID 11929840.

PDB gallery

1iyr: NMR Structure Ensemble Of Dff-C Domain

1koy: NMR structure of DFF-C domain

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This article incorporates text from the public domain Pfam and InterPro IPR015121

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DNA Fragmentation factor 45kDa, C terminal domain Provide feedback

The C terminal domain of DNA Fragmentation factor 45kDa (DFF-C) consists of four alpha-helices, which are folded in a helix-packing arrangement, with alpha-2 and alpha-3 packing against a long C-terminal helix (alpha-4). The main function of this domain is the inhibition of DFF40 by binding to its C-terminal catalytic domain through ionic interactions, thereby inhibiting the fragmentation of DNA in the apoptotic process. In addition to blocking the DNase activity of DFF40, the C-terminal region of DFF45 is also important for the DFF40-specific folding chaperone activity, as demonstrated by the ability of DFF45 to refold DFF40 [1].

Literature references

Fukushima K, Kikuchi J, Koshiba S, Kigawa T, Kuroda Y, Yokoyama S; , J Mol Biol. 2002;321:317-327.: Solution structure of the DFF-C domain of DFF45/ICAD. A structural basis for the regulation of apoptotic DNA fragmentation. PUBMED:12144788 EPMC:12144788

External database links

PANDIT:	PF09033
Pseudofam:	PF09033
SYSTERS:	DFF-C

This tab holds annotation information from the InterPro database.

InterPro entry IPR015121

The C-terminal domain of DNA fragmentation factor 45 kDa (DFF-C) consists of four alpha-helices, which are folded in a helix-packing arrangement, with alpha-2 and alpha-3 packing against a long C-terminal helix (alpha-4). The main function of this domain is the inhibition of DFF40 by binding to its C-terminal catalytic domain through ionic interactions, thereby inhibiting the fragmentation of DNA in the apoptotic process. In addition to blocking the DNase activity of DFF40, the C-terminal region of DFF45 is also important for the DFF40-specific folding chaperone activity, as demonstrated by the ability of DFF45 to refold DFF40 [PUBMED:12144788].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

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PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

	Seed (5)	Full (60)	Representative proteomes				NCBI (53)	Meta (0)
	Seed (5)	Full (60)	RP15 (2)	RP35 (4)	RP55 (11)	RP75 (30)	NCBI (53)	Meta (0)
Jalview	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (5)	Full (60)	Representative proteomes				NCBI (53)	Meta (0)
	Seed (5)	Full (60)	RP15 (2)	RP35 (4)	RP55 (11)	RP75 (30)	NCBI (53)	Meta (0)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (5)	Full (60)	Representative proteomes				NCBI (53)	Meta (0)
	Seed (5)	Full (60)	RP15 (2)	RP35 (4)	RP55 (11)	RP75 (30)	NCBI (53)	Meta (0)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

Seed source:

pdb_1iyr

Previous IDs:

none

Type:

Domain

Author:

Mistry J, Sammut SJ

Number in seed:

5

Number in full:

60

Average length of the domain:

163.20 aa

Average identity of full alignment:

61 %

Average coverage of the sequence by the domain:

53.64 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	25.0	25.0
Trusted cut-off	39.8	39.3
Noise cut-off	23.2	22.4

Model length:

164

Family (HMM) version:

5

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

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Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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Tree controls

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Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the DFF-C domain has been found. There are 2 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: DFF-C (PF09033)

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