The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Accession:
Functional site class:
FFAT motif
Functional site description:
The FFAT motif binds to the Major Sperm Protein (MSP) domain of the integral Endoplasmic Reticulum (ER) membrane proteins Vesicle Associated Membrane Protein (VAMP) Associated Proteins, VAP-A and VAP-B. This motif was initially linked to the targeting of lipid trafficking and lipid sensing proteins to the cytosolic face of the ER. Further studies indicate that VAP-FFAT binding plays a part in the formation of membrane contact sites between the ER and other cellular membranes. Most known instances of FFAT motifs occur in mammal and yeast proteins but additional examples have been reported in pathogenic bacterial and viral proteins. VAP-FFAT interactions may play a role in disease etiology, as mutations in VAP-B have been implicated in late onset Spinal Muscular Atrophy and Amyotrophic Lateral Sclerosis – type 8. Another protein, MOSPD2, which also has an MSP domain has been identified as a second binding partner for FFAT proteins.
ELMs with same func. site: TRG_ER_FFAT_1  TRG_ER_FFAT_2 
ELM Description:
The FFAT motif was initially identified as a short sequence shared between a set of ER-targeted proteins, that was shown to mediate interactions with yeast members of the VAP protein family (Loewen,2003). The consensus core motif was described as EFFDAxE. This core motif is supplemented by a seventh element, the flanking regions (mainly upstream) which contain multiple acidic residues. The acidic tract seems to be crucial for the initial, non-specific binding to the positive surface of the VAP proteins which is further amplified by key residues in the core motif, particularly the residues in the 2nd and 5th positions.

After the original description of the motif, many instances have been reported with various alterations. The second position is the most conserved, tolerating only a phenylalanine or a tyrosine. The aromatic ring of these amino acids binds in a hydrophobic pocket created by the aliphatic side chains of critical VAP residues, including Lys87 and Met89. A second hydrophobic pocket binds the 5th residue of the motif, typically an alanine or a cysteine. Position 3 of the core motif is rather variable, allowing for a number of substitutions.

Aside from the FFAT motif binding with the surface of VAP proteins, a second interaction is revealed in the crystal structure. Two FFAT motifs bind to each other, revealing a “double sandwich” conformation. This bond is mediated by the side chain of the aspartic acid residue in the 4th position of the motif which forms a symmetry related hydrogen bond with the backbone of the aspartic acid of the second FFAT motif. Originally, this position was thought to not tolerate any substitutions but one instance with a glutamic acid replacing the aspartic acid has proven to be functional (Hantan,2014). Additionally, an acidic amino acid is required in the first position. In the structure, this residue seems to interact with the second VAP protein of the dimer.
Pattern: [EDS].{0,4}[ED][FY][FYKREM][DE][AC].{1,2}[EDST]
Pattern Probability: 0.0000103
Present in taxons: Homo sapiens Opisthokonta Rattus norvegicus Saccharomyces cerevisiae Viruses
Interaction Domain:
Motile_Sperm (PF00635) MSP (Major sperm protein) domain (Stochiometry: 1 : 1)
PDB Structure: 1Z9O
o See 29 Instances for TRG_ER_FFAT_1
o Abstract
The Endoplasmic Reticulum (ER) is a dynamic structure that serves as a site of bulk membrane lipid biogenesis for most of the cell organelles with a major portion of lipid production being associated with the cytosolic leaflet of the ER membrane (Baumann,2001). Thus, many proteins with roles in lipid metabolism must access the ER surface. VAP proteins are ER membrane proteins that are highly conserved among eukaryotes, consisting of a C-terminal transmembrane domain, a flexible linker that may contain a short coiled coil, and a cytosolic N-terminal MSP domain (Lev,2008, PF00635). VAPs contribute to the targeting of proteins to the ER through the interaction that occurs between their MSP domain and the FFAT motif of various proteins in both mammals and yeast (Loewen,2003).

Many of the proteins that contain FFAT motifs function in lipid sensing and lipid exchange. Additionally, a role of VAPs in the formation of Membrane Contact Sites (MCSs) has emerged. MCSs are distinct domains between the ER and other organelles where organellar membranes are bridged by proteins (often with a gap less than 30 nm), but do not fuse. MCSs have been proposed to facilitate the non-vesicular trafficking of small molecules, such as lipids (Helle,2013). VAP-FFAT interactions have been shown to control the formation of MCSs between the ER and other cellular membranes, including the plasma membrane, mitochondria, late endosomes, peroxisomes and vesicles that contain uptaken, possibly pathogenic, bacteria.

The 3D structure of the MSP domain-FFAT motif (rat VAP-A with rat ORP1) interaction has been solved using X-ray crystallography (1Z9O). This interaction is mediated by a positive patch on the MSP domain surface, which is strongly conserved (e.g. in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Caenorhabditis elegans and Homo sapiens) in the VAP-family MSP domains, but not in other MSP domains (Loewen,2005). The crystal structure reveals an unusual cooperatively assembled dimer of dimers in a “double peptide sandwich” conformation. FFAT motifs can also bind VAPs as monomers, as was revealed by a more recently obtained solution structure for VAP-A with the FFAT of OSBP (2RR3).
o 11 selected references:

o 8 GO-Terms:

o 29 Instances for TRG_ER_FFAT_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P21957 OPI1
OPI1_YEAST
199 206 DEDDDDEEFFDASEQVNASE TP 15 Saccharomyces cerevisiae (Baker"s yeast)
2 
Q91XL9 Osbpl1a
OSBL1_MOUSE
474 481 VSILSEEEFYDALSGSESEG TP 5 Mus musculus (House mouse)
1 
Q9Y5P4 COL4A3BP
C43BP_HUMAN
319 327 NSLINEEEFFDAVEAALDRQ TP 7 Homo sapiens (Human)
2 
Q9BXW6 OSBPL1A
OSBL1_HUMAN
474 482 SILSEDEFYDALSDSESERS TP 6 Homo sapiens (Human)
1 
Q96RL7 VPS13A
VP13A_HUMAN
839 849 SEDDSEEEFFDAPCSPLEEP TP 6 Homo sapiens (Human)
1 
P43125 rdgB
RDGB_DROME
405 413 KSNSDEEFFDCLDTNETNSL TP 3 Drosophila melanogaster (Fruit fly)
1 
O43681 ASNA1
ASNA_HUMAN
13 20 GWGVEAEEFEDAPDVEPLEP TP 5 Homo sapiens (Human)
1 
O84008 CT_005
Y005_CHLTR
285 293 DSSSSSEYMDALETVAAGDV TP 7 Chlamydia trachomatis D/UW-3/CX
2 
Q9UNN5 FAF1
FAF1_HUMAN
294 301 VSDSDGDDFEDATEFGVDDG TP 7 Homo sapiens (Human)
2 
Q5JSH3 WDR44
WDR44_HUMAN
6 16 ASESDTEEFYDAPEDVHLGG TP 3 Homo sapiens (Human)
2 
Q9XSC3 WDR44
WDR44_BOVIN
6 16 ASESDTEEFFDAPEDVHLEG TP 1 Bos taurus (Cattle)
Q15042 RAB3GAP1
RB3GP_HUMAN
583 591 WSDSEEEFFECLSDTEELKG TP 10 Homo sapiens (Human)
4 
P22059 OSBP
OSBP1_HUMAN
356 364 SDEDDENEFFDAPEIITMPE TP 12 Homo sapiens (Human)
2 
Q709C8 VPS13C
VP13C_HUMAN
876 883 VESESDDEYFDAEDGEPQTC TP 1 Homo sapiens (Human)
Q5T4F4 ZFYVE27
ZFY27_HUMAN
285 293 EAEPDEEFKDAIEETHLVVL TP 9 Homo sapiens (Human)
2 
P38713 OSH3
OSH3_YEAST
511 521 SYLSENDEFFDAEEEISRGV TP 3 Saccharomyces cerevisiae (Baker"s yeast)
Q12451 OSH2
OSH2_YEAST
742 751 EDEASDADEFYDAAELVDEV TP 3 Saccharomyces cerevisiae (Baker"s yeast)
P35845 SWH1
OSH1_YEAST
711 722 ESDEDSDADEFFDAEEAASD TP 7 Saccharomyces cerevisiae (Baker"s yeast)
Q96SU4 OSBPL9
OSBL9_HUMAN
293 300 SYSSSEDEFYDADEFHQSGS TP 6 Homo sapiens (Human)
2 
Q9BZF2 OSBPL7
OSBL7_HUMAN
399 408 LSLADSHTEFFDACEVLLSA TP 2 Homo sapiens (Human)
1 
Q9BZF3 OSBPL6
OSBL6_HUMAN
493 500 SMSESVSEFFDAQEVLLSAS TP 4 Homo sapiens (Human)
2 
Q969R2 OSBP2
OSBP2_HUMAN
447 458 DSEEDEDTEYFDAMEDSTSF TP 2 Homo sapiens (Human)
1 
Q9H4L5 OSBPL3
OSBL3_HUMAN
447 456 LSITDSLSEFFDAQEVLLSP TP 5 Homo sapiens (Human)
1 
Q9H1P3 OSBPL2
OSBL2_HUMAN
5 12 MNGEEEFFDAVTGFDSDNSS TP 2 Homo sapiens (Human)
1 
Q8K4M9 Osbpl1a
OSBL1_RAT
474 481 VSILSEDEFYDALSGSESEG TP 1 Rattus norvegicus (Norway rat)
1 
Q9BZ72 PITPNM2
PITM2_HUMAN
343 351 DESSDDEFFDAHEDLSDTEE TP 2 Homo sapiens (Human)
1 
O00562 PITPNM1
PITM1_HUMAN
348 355 SENSSEEEFFDAHEGFSDSE TP 10 Homo sapiens (Human)
1 
Q9BZ71 PITPNM3
PITM3_HUMAN
31 41 SVESSDDEFFDAREEMAEGK TP 2 Homo sapiens (Human)
1 
Q5SYB0 FRMPD1
FRPD1_HUMAN
767 776 FEDGSSDEEYYDAADKLTPP TP 1 Homo sapiens (Human)
Please cite: The eukaryotic linear motif resource - 2018 update. (PMID:29136216)

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