The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Apple-PAN domain ligand motif
Functional site description:
Factor XI (FXI) acts in the intrinsic pathway of coagulation, it is the zymogen of FXIa, which cleaves Factor IX (FIX). FXI is a disulfide-linked dimer of two subunits, each harbouring four apple domains (A1-4) and a C-terminal trypsin-like catalytic domain. The apple domains assemble into a saucer-shaped disc, where A4 provides the dimerization interface, and the two A2 domains are separated furthest from each other in the FXI dimer. A close homolog of FXI, plasma coagulation factor prekallikrein (PK) has the same domain structure but is a monomeric protein. No other proteins with a similar domain arrangement have been described. Both FXI and PK circulate in complex with a nonenzymatic cofactor, high-molecular-weight kininogen (HK). HK and extracellular matrix components laminin and collagen V employ similar DFP motifs to bind to the 2nd apple domain of FXI and PK.
ELM Description:
The DFP tripeptide motif was derived from a dedicated random peptide-binding screen for coagulation factor XI (FXI) binding. Also, a hydrophobic, aromatic or histidine side chain (F/Y/I/W/H) is preferred two positions ahead of the DFP (Wong,2016). The [FYHWI].DF[PD] motif is only found in a restricted number of extracellular human proteins, including high-molecular weight kininogen (HK), laminin and collagen V (Wong,2016). Of these, HK was already known to act as a cofactor for FXI and to bind the 2nd apple domain (A2; or PAN domain; PFAM: PF00024) of coagulation factor XI (FXI) and plasma kallikrein heavy chain (Tait,1987; Renne,2002; Renne,2002). Surface plasmon resonance (SPR) studies confirmed that full-length heterotrimeric laminin-111, -411, -511 and the DFP motif detected within collagen V specifically bind to FXI (Wong,2016), thus the DFP motif is used by both the cofactor HK and extracellular matrix proteins to interact with FXI and PK.
Structures available for this domain-motif interaction showcase three peptide sequences, one from HK (5I25), one from laminin (5EOD) and one from the random peptide screen (5EOK). The three peptides occupy the same elongated crevice of the 2nd apple domain of FXI and PK. The DFP phenylalanine side chain fits precisely into a major pocket of the domain with the proline and aspartate sidechains also forming contacts. A second interaction is mediated by the residue 2 residues ahead of the core DFP sequence contacting a minor pocket of the apple domain (Wong,2016).
The [FYWHIL].DF[PD] motif pattern is of relatively high confidence and also well represents the results of the peptide screen (it covers 41 of the detected 52 peptides).
Pattern: [FYWHIL].DF[PD]
Pattern Probability: 0.0000220
Present in taxon: Vertebrata
Interaction Domain:
PAN_1 (PF00024) PAN domain (Stochiometry: 1 : 1)
o See 5 Instances for LIG_FXI_DFP_1
o Abstract
The contact activation system (CAS) is central to the crosstalk between coagulation and inflammation and contributes to diverse disorders affecting the cardiovascular system. There are two branches of the CAS: 1) the inflammatory branch activates contact factors FXII and prekallikrein (PK) on the surface of endothelial cells, resulting in the release of the peptide bradykinin (BK), while 2) the plasma coagulation branch activates FXII and FXI on the surface of platelets. CAS factors seem to serve a supportive role in normal hemostasis, rather than a major role in initiating clot formation as evidenced by patients with FXII or FXI deficiency exhibiting no severe bleeding tendencies (Pathak,2018).
Factor XI (FXI) is the zymogen of a plasma protease, factor XIa (FXIa) that contributes to thrombin generation during blood coagulation by proteolytic activation of several coagulation factors, and most notably factor IX (FIX). FXI is structurally distinct from the vitamin K-dependent proteases that form the core of the vertebrate coagulation mechanism. Rather, it is a close homolog of prekallikrein (PK), a component of the plasma kallikrein-kinin system. Since the duplication of the ancestral gene FXI has undergone important structural changes that are required for its procoagulant activities (Mohammed,2018; Pathak,2018; Wong,2016). Uniquely among coagulation factors, FXI circulates as a disulfide-linked dimer. Each subunit has four apple domains (A1-4) (also named PAN domains PFAM: PF00024) and a C-terminal trypsin-like catalytic domain. Each apple domain consists of seven β-strands supporting a single α-helix, and the four of them assemble into a saucer-shaped disc. While A4 domains provide the dimerization interface, the two A2 domains are separated furthest from each other in the FXI dimer. PK has the same domain structure but is a monomeric protein. No other proteins with a similar domain arrangement have been described (Wong,2016).
Almost all FXI and most of PK circulate in complex with high molecular weight kininogen (HK), a highly glycosylated 120-kDa plasma protein with 6 domains. The physiologic importance of the PK-HK interaction seems clear as HK cleavage by α-kallikrein (activated PK) liberates the vasoactive peptide bradykinin from HK, and HK enhances PK activation by FXIIa. The importance of the FXI-HK interaction is less clear (Mohammed,2018).
Early studies identified that a region within the C-terminal D6 domain of HK, with at least 58 amino acids (HK residues 556-613) is required for normal FXI binding, and 31 amino acids for PK binding (Tait,1987), is responsible for the binding of FXI and PK A2 domains (Renne,2002; Renne,2002).
A dedicated random peptide-binding screen with FXI identified the DFP core motif (precisely a [FYWHIL].DF [PD] motif pattern) as an optimal binding partner for FXI (Wong,2016). This DFP motif was then detected not only within the C-terminal D6 domain of HK, but also in other extracellular proteins that could potentially interact with FXI and PK, e.g. laminin and collagen V. X-ray structures of the complexes between FXI and the corresponding motif of HK (5I25), laminin A1 (5EOD), and P39 peptide from the random screen (5EOK) show that the motifs bind to the same site on FXI. The Phe residue of the DFP occupies a major hydrophobic pocket, while the hydrophobic/aromatic residue preceding the DFP core motif inserts into a more minor pocket on the 2nd apple domain of FXI. The dimeric FXI orients 2 bound DFP peptides onto the same surface (Wong,2016). Surface plasmon resonance (SPR) studies also confirmed the binding of full-length heterotrimeric complexes, laminin-111, -411 and -511 to FXI, as well as the binding of a second motif instance within HK and one in collagen V (Wong,2016).
Efficient coagulation factor cleavage reactions typically take place only on a designated surface. While vitamin K–dependent coagulation factors have an N-terminal Gla domain that is capable of binding directly to negatively charged phospholipids present in activated platelets, FXI does not have a dedicated domain for this purpose. Laminins play important roles in plasma coagulation and thrombus formation, and the interaction between platelet integrins and laminins has been well characterized. Also, laminin has been previously shown to provide a surface that can promote plasma coagulation and thrombus formation in the absence of platelets (Schaff,2013; White-Adams,2010). Finally, HK and coagulation FXII (which activates FXI) have both previously been reported to bind laminin (Schousboe,2006; Schousboe,2009). Therefore the interactions observed for FXI with laminin and collagen V are most probably important for its colocalization with other intrinsic pathway coagulation factors to sites in the extracellular matrix (Wong,2016).
In sum, the HK cofactor and components of the extracellular matrix all seem to employ DFP motifs to interact with FXI and PK (Wong,2016).
o 10 selected references:

o 7 GO-Terms:

o 5 Instances for LIG_FXI_DFP_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P12107 COL11A1
1614 1618 CKDLQLSHPDFPDGEYWIDP U 1 Homo sapiens (Human)
P20908 COL5A1
1646 1650 CKDLQLCHPDFPDGEYWVDP TP 1 Homo sapiens (Human)
P25391 LAMA1
2191 2195 SGSTRLEFPDFPIDDNRWHS TP 2 Homo sapiens (Human)
P25391 LAMA1
1081 1085 CDQCSLGYRDFPDCVPCDCD U 1 Homo sapiens (Human)
P01042 KNG1
603 607 NGLSFNPISDFPDTTSPKCP TP 4 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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