PMC:3405059 / 19328-23394 JSONTXT

{"project":"2_test","denotations":[{"id":"22848655-20727575-88310298","span":{"begin":140,"end":142},"obj":"20727575"},{"id":"22848655-20881961-88310299","span":{"begin":146,"end":148},"obj":"20881961"},{"id":"22848655-15167892-88310300","span":{"begin":152,"end":154},"obj":"15167892"},{"id":"22848655-20457744-88310301","span":{"begin":175,"end":177},"obj":"20457744"},{"id":"22848655-8578593-88310302","span":{"begin":181,"end":183},"obj":"8578593"},{"id":"22848655-20877282-88310303","span":{"begin":443,"end":445},"obj":"20877282"},{"id":"22848655-12925274-88310304","span":{"begin":707,"end":709},"obj":"12925274"},{"id":"22848655-15582390-88310305","span":{"begin":713,"end":715},"obj":"15582390"},{"id":"22848655-12958590-88310306","span":{"begin":719,"end":721},"obj":"12958590"},{"id":"22848655-15582390-88310307","span":{"begin":1202,"end":1204},"obj":"15582390"},{"id":"22848655-15358240-88310308","span":{"begin":3177,"end":3179},"obj":"15358240"},{"id":"T21242","span":{"begin":140,"end":142},"obj":"20727575"},{"id":"T23804","span":{"begin":146,"end":148},"obj":"20881961"},{"id":"T28413","span":{"begin":152,"end":154},"obj":"15167892"},{"id":"T24437","span":{"begin":175,"end":177},"obj":"20457744"},{"id":"T96428","span":{"begin":181,"end":183},"obj":"8578593"},{"id":"T5422","span":{"begin":443,"end":445},"obj":"20877282"},{"id":"T94121","span":{"begin":707,"end":709},"obj":"12925274"},{"id":"T10618","span":{"begin":713,"end":715},"obj":"15582390"},{"id":"T71548","span":{"begin":719,"end":721},"obj":"12958590"},{"id":"T37628","span":{"begin":1202,"end":1204},"obj":"15582390"},{"id":"T83041","span":{"begin":3177,"end":3179},"obj":"15358240"}],"text":"Overall Structure\nThe RON Sema domain adopts the seven-bladed β-propeller fold, found in Met, semaphorins and plexin receptors (Figure 1A) [61], [62], [63]. The DALI program [64], [65] identified the Met Sema domain (PDB code 1SHY) as the closest to the RON Sema domain, with Z = 41.1 and root mean square deviation (RMSD) of 3.1 Å for 462 Cα atoms. More distant structural homologues of RON Sema include the plexin receptors and semaphorins [66]. RON Sema contains hallmark features of the Sema-type β-propeller. These features include a large insertion, termed extrusion, in the 5th blade and deviations from four antiparallel β strands, characteristic of the individual β-sheets in the β-propeller fold [67], [68], [69]. In RON and Met Sema domains, blade 5 of the β-propeller contains three β-strands (strands A–C) and blades 4 and 6 contain five β-strands (strands A–E) with strand A being the innermost β-strand at the center of β-propeller (Figure 1A). The N-terminal residues (Val42–Tyr44) provide the 5th β-strand (β6E) of blade 6. The extrusion regions in blade 5 vary both in sequence and length in different Sema-type β-propellers, ranging from 57 residues in Met to 77 residues in Sema4D [68]. In RON, the 62-residue insertion (Pro370–Ser432) is located between β-strands 5C and 4E (Figure 2), and it forms a 16-residue helix (αEX1), followed by a long loop that packs tightly against the outermost 4E (Figure 1A). Structural integrity of this long loop is maintained by two adjacent disulfide bonds (Cys385–Cys407 and Cys386–Cys422) and by stacking of aromatic groups (Phe400 of the extrusion and Tyr245 of α-helix 3D of the core Sema domain). Electrostatic potential analysis showed that the top surface of the β-propeller barrel, corresponding to loop segments connecting the β-strands BC and DA, and the sides of the barrel are neutral. In contrast, the bottom surface of the β-propeller barrel, corresponding to loop segments connecting the AB and CD β-strands is negatively charged (Figure 1B). The pronounced negatively charged surface suggests interaction with a positively charged region of a counterpart protein.\n10.1371/journal.pone.0041912.g002 Figure 2 Structure-based sequence alignments of human RON and Met Sema-PSI.\nResidues are colored as follows: Identical residues (red), and conservatively replaced residues (blue) are boxed. Cysteines are colored gold. Matching colored symbols indicate pairs of cysteines that form disulfide bonds. Secondary structure units of RON and Met are labeled. The blue dots above the RON Sema residues indicate amino acids at the symmetry-related RON Sema-Sema interface as discussed in the text. The blue dots below the Met Sema sequence show residues that contact the HGFβ ligand (PDB code 1SHY) (Stamos et al., 2004). This figure was prepared with ESPript (espript.ibcp.fr/Espript/). A small, cysteine-rich PSI motif follows the Sema domains of both RON and Met receptor tyrosine kinases. PSI modules, found in the extracellular domains of over 1,600 structurally and functionally related receptor proteins, serve as hinges to orient the preceding and ensuing domains for proper receptor-ligand interactions [70]. The PSI motifs of RON and Met adopt a cysteine-knot fold consisting of two small antiparallel β-sheets and four short α-helices (Figure 1A). RON PSI contains 8 conserved cysteines, which form four disulfide linkages (Cys527–Cys545, Cys536–Cys552, Cys548–Cys558, and Cys533–Cys567 in RON sequence). A DALI alignment of the RON and Met PSI domains yielded Z = 8.0 and RMSD = 1.5 Å for 44 paired Cα atoms. RON PSI motif shows a negatively charged surface on one side as it extends from RON Sema’s bottom surface (Figure 1B, right panel), while positive charged residues populate the opposite surface of the PSI motif (Figure 1B, left panel). The interdomain contact area between the RON Sema and PSI domains embeds ∼385 Å2 surface area. The small interaction surface is consistent with a flexible module that mediates the conformational transition of multi-domain cell surface receptors."}