Structures of heparin-derived tetrasaccharide bound to cobra cardiotoxins: heparin binding at a single protein site with diverse side chain interactions.
Cobra cardiotoxins (CTXs) are three-fingered polypeptides with positively charged domains that have been shown to bind to anionic ligands of snake venom citrate, glycosaminoglycans, sulfoglycosphingolipid, and nucleotide triphosphate with various biochemical effects including toxin dimerization, cell surface retention, membrane pore formation, cell internalization and blocking of enzymatic activities of kinase and ATPase. The reported anionic binding sites, however, are found to be different among different CTX homologues for potentially different CTX activities. Herein, by NMR studies of the binding of inorganic phosphate, dATP (stable form of ATP), and heparin-derived tetrasaccharide to Naja atra CTX A1, a novel CTX molecule exhibiting in vivo necrotic activity on skeletal muscle, we demonstrate that diverse ligands binding to CTXs could also occur at a single protein site with flexible side chain interactions. The flexibility of such an interaction is also illustrated by the available heparin-CTX A3 complex structures with different heparin chain lengths binding at the same site. Our results provide a likely structural explanation on how the interaction between heparan sufate and proteins depends more on the overall charge cluster organization rather than on their fine structures. We also suggest that the ligand binding site of CTX homologues can be fine-tuned by nonconserved residues near the binding pocket because of their flexible side chain interaction and dimerization ability, even for the rigid CTX molecules tightened by four disulfide bonds.
Tjong
Siu-Cin
SC
Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsin Chu 30043, Taiwan.
Chen
Ting-Shou
TS
Huang
Wei-Ning
WN
Wu
Wen-Guey
WG
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D004179:Cobra Cardiotoxin Proteins / Q000737:chemistry* / Q000302:isolation & purification / Q000633:toxicity; D004546:Elapid Venoms / Q000737:chemistry; D006493:Heparin / Q000737:chemistry* / Q000378:metabolism*; D006497:Heparan Sulfate / Q000378:metabolism*; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000737:chemistry / Q000378:metabolism*; D010710:Phosphates / Q000737:chemistry / Q000378:metabolism; D011134:Polysaccharides / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid; D013329:Structure-Activity Relationship
D004179:Cobra Cardiotoxin Proteins; D004546:Elapid Venoms; D006493:Heparin; D006497:Heparan Sulfate; D008024:Ligands; D009711:Nucleotides; D010710:Phosphates; D011134:Polysaccharides