Summary: Formin Homology 2 Domain

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Wikipedia: Formins
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Formins Edit Wikipedia article

formin 1
Identifiers
Symbol	FMN1
Alt. symbols	LD, FMN
Entrez	342184
HUGO	3768
OMIM	136535
RefSeq	NM_001103184
UniProt	Q68DA7
Other data
Locus	Chr. 15 q13-q14

formin 2
Identifiers
Symbol	FMN2
Entrez	56776
HUGO	14074
OMIM	606373
RefSeq	XM_371352
UniProt	Q9NZ56
Other data
Locus	Chr. 1 q43

Domain structure of formin proteins across phyla.^[1]

Formin Homology Region 1

Identifiers

Symbol

Drf_FH1

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

Formin Homology 2 Domain

crystal structures of a formin homology-2 domain reveal a tethered-dimer architecture

Identifiers

Symbol

FH2

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

Diaphanous FH3 Domain

crystal structure of mdia1 gbd-fh3 in complex with rhoc-gmppnp

Identifiers

Symbol

Drf_FH3

Pfam clan

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

DRF Autoregulatory Domain

crystal structure of the n-terminal mdia1 armadillo repeat region and dimerisation domain in complex with the mdia1 autoregulatory domain (dad)

Identifiers

Symbol

Drf_DAD

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

Diaphanous GTPase-binding Domain

crystal structure of mdia1 gbd-fh3 in complex with rhoc-gmppnp

Identifiers

Symbol

Drf_GBD

Pfam clan

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

Formins (formin homology proteins) are a group of proteins that are involved in the polymerization of actin and associate with the fast-growing end (barbed end) of actin filaments.^[2] Most formins are Rho-GTPase effector proteins. Formins regulate the actin and microtubule cytoskeleton ^[3]^[4] and are involved in various cellular functions such as cell polarity, cytokinesis, cell migration and SRF transcriptional activity.^[5] Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus.

Diversity

Formins have been found in all eukaryotes studied.^[1] In humans, 15 different formin proteins are present that have been classified in 7 subgroups.^[6] By contrast, yeasts contain only 2-3 formins.^[7]

Structure and interactions

Formins are characterised by the presence of three formin homology (FH) domains (FH1, FH2 and FH3), although members of the formin family do not necessarily contain all three domains.^[8]^[9] In addition, other domains are usually present, such as PDZ, DAD, WH2, or FHA domains.

The proline-rich FH1 domain mediates interactions with a variety of proteins, including the actin-binding protein profilin, SH3 (Src homology 3) domain proteins,^[10] and WW domain proteins. The actin nucleation-promoting activity of S. cerevisiae formins has been localized to the FH2 domain.^[4] The FH2 domain is required for the self-association of formin proteins through the ability of FH2 domains to directly bind each other, and may also act to inhibit actin polymerisation.^[11]^[12] The FH3 domain is less well conserved and is required for directing formins to the correct intracellular location, such the mitotic spindle, or the projection tip during conjugation.^[13]^[14] In addition, some formins can contain a GTPase-binding domain (GBD) required for binding to Rho small GTPases, and a C-terminal conserved DRF autoregulatory domain (Dia-autoregulatory domain) (DAD). The GBD domain is a bifunctional autoinhibitory domain that interacts with and is regulated by activated Rho family members. Mammalian Drf3 contains a CRIB-like motif within its GBD for binding to Cdc42, which is required for Cdc42 to activate and guide Drf3 towards the cell cortex where it remodels the actin skeleton.^[15] The DRF autoregulatory domain binds the N-terminal GTPase-binding domain; this link is broken when GTP-bound Rho binds to the GBD and activates the protein. The addition of the DAD to mammalian cells induces actin filament formation, stabilises microtubules, and activates serum-response mediated transcription.^[15] Another commonly found domain is an armadillo repeat region (ARR) located in the FH3 domain.

The FH2 domain, has been shown by X-ray crystallography to have an elongated, crescent shape containing three helical subdomains.^[16]^[17]

Formins also directly bind to microtubules via their FH2 domain. This interaction is important in promoting the capture and stabilization of a subset of microtubules oriented towards the leading edge of migrating cells. Formins also promote the capture of microtubules by the kinetochore during mitosis and for aligning microtubules along actin filaments.^[18]^[19]

References

^ ^a ^b Chalkia D, Nikolaidis N, Makalowski W, Klein J, Nei M (December 2008). "Origins and evolution of the formin multigene family that is involved in the formation of actin filaments". Molecular Biology and Evolution. 25 (12): 2717–33. doi:10.1093/molbev/msn215. PMC 2721555. PMID 18840602.
^ Evangelista M, Zigmond S, Boone C (July 2003). "Formins: signaling effectors for assembly and polarization of actin filaments". Journal of Cell Science. 116 (Pt 13): 2603–11. doi:10.1242/jcs.00611. PMID 12775772.
^ Gunning PW, Ghoshdastider U, Whitaker S, Popp D, Robinson RC (June 2015). "The evolution of compositionally and functionally distinct actin filaments". Journal of Cell Science. 128 (11): 2009–19. doi:10.1242/jcs.165563. PMID 25788699.
^ ^a ^b Goode BL, Eck MJ (2007). "Mechanism and function of formins in the control of actin assembly". Annual Review of Biochemistry. 76: 593–627. doi:10.1146/annurev.biochem.75.103004.142647. PMID 17373907.
^ Faix J, Grosse R (June 2006). "Staying in shape with formins". Developmental Cell. 10 (6): 693–706. doi:10.1016/j.devcel.2006.05.001. PMID 16740473.
^ Higgs HN, Peterson KJ (January 2005). "Phylogenetic analysis of the formin homology 2 domain". Molecular Biology of the Cell. 16 (1): 1–13. doi:10.1091/mbc.E04-07-0565. PMC 539145. PMID 15509653.
^ Baarlink C, Brandt D, Grosse R (July 2010). "SnapShot: Formins". Cell. 142 (1): 172, 172.e1. doi:10.1016/j.cell.2010.06.030. PMID 20603022.
^ Kitayama C, Uyeda TQ (February 2003). "ForC, a novel type of formin family protein lacking an FH1 domain, is involved in multicellular development in Dictyostelium discoideum". Journal of Cell Science. 116 (Pt 4): 711–23. doi:10.1242/jcs.00265. PMID 12538772.
^ Wallar BJ, Alberts AS (August 2003). "The formins: active scaffolds that remodel the cytoskeleton". Trends in Cell Biology. 13 (8): 435–46. doi:10.1016/S0962-8924(03)00153-3. PMID 12888296.
^ Uetz P, Fumagalli S, James D, Zeller R (December 1996). "Molecular interaction between limb deformity proteins (formins) and Src family kinases". The Journal of Biological Chemistry. 271 (52): 33525–30. doi:10.1074/jbc.271.52.33525. PMID 8969217.
^ Takeya R, Sumimoto H (November 2003). "Fhos, a mammalian formin, directly binds to F-actin via a region N-terminal to the FH1 domain and forms a homotypic complex via the FH2 domain to promote actin fiber formation". Journal of Cell Science. 116 (Pt 22): 4567–75. doi:10.1242/jcs.00769. PMID 14576350.
^ Shimada A, Nyitrai M, Vetter IR, Kühlmann D, Bugyi B, Narumiya S, Geeves MA, Wittinghofer A (February 2004). "The core FH2 domain of diaphanous-related formins is an elongated actin binding protein that inhibits polymerization". Molecular Cell. 13 (4): 511–22. doi:10.1016/S1097-2765(04)00059-0. PMID 14992721.
^ Kato T, Watanabe N, Morishima Y, Fujita A, Ishizaki T, Narumiya S (February 2001). "Localization of a mammalian homolog of diaphanous, mDia1, to the mitotic spindle in HeLa cells". Journal of Cell Science. 114 (Pt 4): 775–84. PMID 11171383.
^ Petersen J, Nielsen O, Egel R, Hagan IM (June 1998). "FH3, a domain found in formins, targets the fission yeast formin Fus1 to the projection tip during conjugation". The Journal of Cell Biology. 141 (5): 1217–28. doi:10.1083/jcb.141.5.1217. PMC 2137179. PMID 9606213.
^ ^a ^b Peng J, Wallar BJ, Flanders A, Swiatek PJ, Alberts AS (April 2003). "Disruption of the Diaphanous-related formin Drf1 gene encoding mDia1 reveals a role for Drf3 as an effector for Cdc42". Current Biology. 13 (7): 534–45. doi:10.1016/S0960-9822(03)00170-2. PMID 12676083.
^ Xu Y, Moseley JB, Sagot I, Poy F, Pellman D, Goode BL, Eck MJ (March 2004). "Crystal structures of a Formin Homology-2 domain reveal a tethered dimer architecture". Cell. 116 (5): 711–23. doi:10.1016/S0092-8674(04)00210-7. PMID 15006353.
^ Thompson ME, Heimsath EG, Gauvin TJ, Higgs HN, Kull FJ (January 2013). "FMNL3 FH2-actin structure gives insight into formin-mediated actin nucleation and elongation". Nature Structural & Molecular Biology. 20 (1): 111–8. doi:10.1038/nsmb.2462. PMC 3876896. PMID 23222643.
^ Palazzo AF, Cook TA, Alberts AS, Gundersen GG (August 2001). "mDia mediates Rho-regulated formation and orientation of stable microtubules". Nature Cell Biology. 3 (8): 723–9. doi:10.1038/35087035. PMID 11483957.
^ Bartolini F, Gundersen GG (February 2010). "Formins and microtubules". Biochimica et Biophysica Acta. 1803 (2): 164–73. doi:10.1016/j.bbamcr.2009.07.006. PMC 2856479. PMID 19631698.

External links

MBInfo - Formin mediated actin nucleation

This article incorporates text from the public domain Pfam and InterPro IPR010472

This article incorporates text from the public domain Pfam and InterPro IPR015425

This article incorporates text from the public domain Pfam and InterPro IPR010465

This article incorporates text from the public domain Pfam and InterPro IPR010473

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Formin Homology 2 Domain Provide feedback

No Pfam abstract.

Internal database links

SCOOP:

APG6 Baculo_PEP_C DUF1241 EzrA IncA Reo_sigmaC Spc7

External database links

SCOP:	1ux5
SMART:	FH2

This tab holds annotation information from the InterPro database.

InterPro entry IPR015425

Formin homology (FH) proteins play a crucial role in the reorganisation of the actin cytoskeleton, which mediates various functions of the cell cortex including motility, adhesion, and cytokinesis [PUBMED:10631086]. Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus. Formins are characterised by the presence of three FH domains (FH1, FH2 and FH3), although members of the formin family do not necessarily contain all three domains [PUBMED:12538772]. The proline-rich FH1 domain mediates interactions with a variety of proteins, including the actin-binding protein profilin, SH3 (Src homology 3) domain proteins, and WW domain proteins. The FH2 domain is required for the self-association of formin proteins through the ability of FH2 domains to directly bind each other [PUBMED:14576350], and may also act to inhibit actin polymerisation [PUBMED:14992721]. The FH3 domain (INTERPRO) is less well conserved and may be important for determining intracellular localisation of formin family proteins. In addition, some formins can contain a GTPase-binding domain (GBD) (INTERPRO) required for binding to Rho small GTPases, and a C-terminal conserved Dia-autoregulatory domain (DAD).

This entry represents the FH2 domain, which was shown by X-ray crystallography to have an elongated, crescent shape containing three helical subdomains [PUBMED:15006353].

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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
UniProt: alignment generated by searching the UniProtKB sequence database using the family HMM
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.

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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 (41)	Full (5365)	Representative proteomes				UniProt (8065)	NCBI (14961)	Meta (30)
	Seed (41)	Full (5365)	RP15 (1370)	RP35 (2723)	RP55 (4101)	RP75 (4903)	UniProt (8065)	NCBI (14961)	Meta (30)
Jalview	View	View	View	View	View	View	View	View	View
HTML	View
PP/heatmap	₁

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

Key: available, not generated, — not available.

Format an alignment

	Seed (41)	Full (5365)	Representative proteomes				UniProt (8065)	NCBI (14961)	Meta (30)
	Seed (41)	Full (5365)	RP15 (1370)	RP35 (2723)	RP55 (4101)	RP75 (4903)	UniProt (8065)	NCBI (14961)	Meta (30)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
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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 (41)	Full (5365)	Representative proteomes				UniProt (8065)	NCBI (14961)	Meta (30)
	Seed (41)	Full (5365)	RP15 (1370)	RP35 (2723)	RP55 (4101)	RP75 (4903)	UniProt (8065)	NCBI (14961)	Meta (30)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	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.

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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:

Alignment kindly provided by SMART

Previous IDs:

none

Type:

Family

Author:

SMART

Number in seed:

41

Number in full:

5365

Average length of the domain:

325.90 aa

Average identity of full alignment:

21 %

Average coverage of the sequence by the domain:

32.77 %

HMM information

HMM build commands:

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

search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	25.3	25.3
Trusted cut-off	25.3	25.3
Noise cut-off	25.2	25.2

Model length:

372

Family (HMM) version:

22

Download:

download the raw HMM for this family

Species distribution

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Archea	Eukaryota
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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:

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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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There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

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.

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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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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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Interactions

There are 3 interactions for this family. More...

Actin Drf_FH3 FH2

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 FH2 domain has been found. There are 25 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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Family: FH2 (PF02181)

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Summary: Formin Homology 2 Domain

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Formins Edit Wikipedia article

Contents

Diversity

Structure and interactions

References

External links

Formin Homology 2 Domain Provide feedback

Internal database links

External database links

InterPro entry IPR015425

Domain organisation

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

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Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

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Sub-species

Too many species/sequences

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Annotation

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Selected sequences

Species trees

Interactive tree

Interactions

Structures