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The structure of the Ca²+-binding, glycosylated F-spondin domain of F-spondin - A C2-domain variant in an extracellular matrix protein.

Tan K, Lawler J - BMC Struct. Biol. (2011)

Bottom Line: The FS domain is found in F-spondins, mindins, M-spondin and amphiF-spondin.The unique feature of F-spondin FS domain is the presence of three disulfide bonds associated with the N- and C-termini of the domain and a highly conserved N-linked glycosylation site.The integrin-binding motif found in mindin is not conserved in the F-spondin FS domain.

View Article: PubMed Central - HTML - PubMed

Affiliation: Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA. ktan@anl.gov

ABSTRACT

Background: F-spondin is a multi-domain extracellular matrix (ECM) protein and a contact-repellent molecule that directs axon outgrowth and cell migration during development. The reelin_N domain and the F-spondin domain (FS domain) comprise a proteolytic fragment that interacts with the cell membrane and guides the projection of commissural axons to floor plate. The FS domain is found in F-spondins, mindins, M-spondin and amphiF-spondin.

Results: We present the crystal structure of human F-spondin FS domain at 1.95Å resolution. The structure reveals a Ca2+-binding C2 domain variant with an 8-stranded antiparallel β-sandwich fold. Though the primary sequences of the FS domains of F-spondin and mindin are less than 36% identical, their overall structures are very similar. The unique feature of F-spondin FS domain is the presence of three disulfide bonds associated with the N- and C-termini of the domain and a highly conserved N-linked glycosylation site. The integrin-binding motif found in mindin is not conserved in the F-spondin FS domain.

Conclusion: The structure of the F-spondin FS domain completes the structural studies of the multiple-domain ECM molecule. The homology of its core structure to a common Ca2+- and lipid-binding C2 domain suggests that the F-spondin FS domain may be responsible for part of the membrane targeting of F-spondin in its regulation of axon development. The structural properties of the FS domain revealed in this study pave the way for further exploration into the functions of F-spondin.

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The top of the FS domain. Besides Ca2+-binding site, two of three SO42- groups (from crystallization buffer) identified in the structure are associated with R226 and R227 on one side of the top of the FS domain. The top of the FS domain is also rich in aromatic residues and prolines. The β7-β8 loop covers most the of FS domain on one side. When it turns at Y363, the sidechain of Y363 dips into a pocket containing aromatic residues and prolines, including P388 and F389. After the β7" short strand, four rings from H384, P385, Y390 and P392 are parallel to each other in a row. Additional aromatic residues from other loops are also found on the top of the domain, including W215, W231, P324, W326, P352, W353, Y363 and F383. All of these residues are either identical or highly conserved in the FS domains of other proteins (Figure 4). The role of these aromatic residues is unknown.
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Figure 3: The top of the FS domain. Besides Ca2+-binding site, two of three SO42- groups (from crystallization buffer) identified in the structure are associated with R226 and R227 on one side of the top of the FS domain. The top of the FS domain is also rich in aromatic residues and prolines. The β7-β8 loop covers most the of FS domain on one side. When it turns at Y363, the sidechain of Y363 dips into a pocket containing aromatic residues and prolines, including P388 and F389. After the β7" short strand, four rings from H384, P385, Y390 and P392 are parallel to each other in a row. Additional aromatic residues from other loops are also found on the top of the domain, including W215, W231, P324, W326, P352, W353, Y363 and F383. All of these residues are either identical or highly conserved in the FS domains of other proteins (Figure 4). The role of these aromatic residues is unknown.

Mentions: The core of the FS domain has an 8-stranded β-sandwich fold, with strands β4, β1, β8, and β7 forming one β-sheet and strands β3, β2, β5 and β6 forming the other sheet (Figure 2). The topology represents one of two types of C2 domain β-sandwich folds[22]. The first major variation of the FS domain, as compared to a common C2 domain, is its long linker (38 amino acids) between β2 and β3 strands, which actually forms two anti-parallel α-helices, packed against the β3/β2/β5/β6 sheet. The second variation is its long linker (51 amino acids) between the β7 and β8 strands. The linker first crosses over to the β3/β2/β5/β6 sheet and forms a short strand, β7' (W353D354) that is anti-parallel to the edge strand, β6 (Figure 2 and 3). It then runs above the β5-β6 loop and turns back at Y363. The linker forms a second short strand, β7" (R377-P378), by β7'. The addition of the two short strands is an expansion of the β3/β2/β5/β6 sheet to a 6-stranded sheet. Additionally, a part of the loop between β2 and α1 (G249-G250) runs in an anti-parallel fashion by the β7" strand, forming two mainchain-mainchain hydrogen bonds with the residue I376 right before β7". These two interactions (G249 N- I374 O and G250 O-I374 N) do not define another β strand.


The structure of the Ca²+-binding, glycosylated F-spondin domain of F-spondin - A C2-domain variant in an extracellular matrix protein.

Tan K, Lawler J - BMC Struct. Biol. (2011)

The top of the FS domain. Besides Ca2+-binding site, two of three SO42- groups (from crystallization buffer) identified in the structure are associated with R226 and R227 on one side of the top of the FS domain. The top of the FS domain is also rich in aromatic residues and prolines. The β7-β8 loop covers most the of FS domain on one side. When it turns at Y363, the sidechain of Y363 dips into a pocket containing aromatic residues and prolines, including P388 and F389. After the β7" short strand, four rings from H384, P385, Y390 and P392 are parallel to each other in a row. Additional aromatic residues from other loops are also found on the top of the domain, including W215, W231, P324, W326, P352, W353, Y363 and F383. All of these residues are either identical or highly conserved in the FS domains of other proteins (Figure 4). The role of these aromatic residues is unknown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3117680&req=5

Figure 3: The top of the FS domain. Besides Ca2+-binding site, two of three SO42- groups (from crystallization buffer) identified in the structure are associated with R226 and R227 on one side of the top of the FS domain. The top of the FS domain is also rich in aromatic residues and prolines. The β7-β8 loop covers most the of FS domain on one side. When it turns at Y363, the sidechain of Y363 dips into a pocket containing aromatic residues and prolines, including P388 and F389. After the β7" short strand, four rings from H384, P385, Y390 and P392 are parallel to each other in a row. Additional aromatic residues from other loops are also found on the top of the domain, including W215, W231, P324, W326, P352, W353, Y363 and F383. All of these residues are either identical or highly conserved in the FS domains of other proteins (Figure 4). The role of these aromatic residues is unknown.
Mentions: The core of the FS domain has an 8-stranded β-sandwich fold, with strands β4, β1, β8, and β7 forming one β-sheet and strands β3, β2, β5 and β6 forming the other sheet (Figure 2). The topology represents one of two types of C2 domain β-sandwich folds[22]. The first major variation of the FS domain, as compared to a common C2 domain, is its long linker (38 amino acids) between β2 and β3 strands, which actually forms two anti-parallel α-helices, packed against the β3/β2/β5/β6 sheet. The second variation is its long linker (51 amino acids) between the β7 and β8 strands. The linker first crosses over to the β3/β2/β5/β6 sheet and forms a short strand, β7' (W353D354) that is anti-parallel to the edge strand, β6 (Figure 2 and 3). It then runs above the β5-β6 loop and turns back at Y363. The linker forms a second short strand, β7" (R377-P378), by β7'. The addition of the two short strands is an expansion of the β3/β2/β5/β6 sheet to a 6-stranded sheet. Additionally, a part of the loop between β2 and α1 (G249-G250) runs in an anti-parallel fashion by the β7" strand, forming two mainchain-mainchain hydrogen bonds with the residue I376 right before β7". These two interactions (G249 N- I374 O and G250 O-I374 N) do not define another β strand.

Bottom Line: The FS domain is found in F-spondins, mindins, M-spondin and amphiF-spondin.The unique feature of F-spondin FS domain is the presence of three disulfide bonds associated with the N- and C-termini of the domain and a highly conserved N-linked glycosylation site.The integrin-binding motif found in mindin is not conserved in the F-spondin FS domain.

View Article: PubMed Central - HTML - PubMed

Affiliation: Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA. ktan@anl.gov

ABSTRACT

Background: F-spondin is a multi-domain extracellular matrix (ECM) protein and a contact-repellent molecule that directs axon outgrowth and cell migration during development. The reelin_N domain and the F-spondin domain (FS domain) comprise a proteolytic fragment that interacts with the cell membrane and guides the projection of commissural axons to floor plate. The FS domain is found in F-spondins, mindins, M-spondin and amphiF-spondin.

Results: We present the crystal structure of human F-spondin FS domain at 1.95Å resolution. The structure reveals a Ca2+-binding C2 domain variant with an 8-stranded antiparallel β-sandwich fold. Though the primary sequences of the FS domains of F-spondin and mindin are less than 36% identical, their overall structures are very similar. The unique feature of F-spondin FS domain is the presence of three disulfide bonds associated with the N- and C-termini of the domain and a highly conserved N-linked glycosylation site. The integrin-binding motif found in mindin is not conserved in the F-spondin FS domain.

Conclusion: The structure of the F-spondin FS domain completes the structural studies of the multiple-domain ECM molecule. The homology of its core structure to a common Ca2+- and lipid-binding C2 domain suggests that the F-spondin FS domain may be responsible for part of the membrane targeting of F-spondin in its regulation of axon development. The structural properties of the FS domain revealed in this study pave the way for further exploration into the functions of F-spondin.

Show MeSH
Related in: MedlinePlus