PDBsum entry 2es3

Sugar binding protein

PDB id

2es3

Contents

			Protein chain

					209 a.a.

			Waters ×257

References listed in PDB file

Key reference

Title

Heparin-Induced cis- And trans- Dimerization modes of the thrombospondin-1 n-Terminal domain.

Authors

K.Tan, M.Duquette, J.H.Liu, K.Shanmugasundaram, A.Joachimiak, J.T.Gallagher, A.C.Rigby, J.H.Wang, J.Lawler.

Ref.

J Biol Chem, 2007, 283, 3932-3941. [DOI no: 10.1074/jbc.M705203200]

PubMed id

18065761

Abstract

Through its interactions with proteins and proteoglycans, thrombospondin-1 (TSP-1) functions at the interface of the cell membrane and the extracellular matrix to regulate matrix structure and cellular phenotype. We have previously determined the structure of the high affinity heparin-binding domain of TSP-1, designated TSPN-1, in association with the synthetic heparin, Arixtra. To establish that the binding of TSPN-1 to Arixtra is representative of the association with naturally occurring heparins, we have determined the structures of TSPN-1 in complex with heparin oligosaccharides containing eight (dp8) and ten (dp10) subunits, by X-ray crystallography. We have found that (1) dp8 and dp10 bind to TSPN-1 in a manner similar to Arixtra, and (2) dp8 and dp10 induce the formation of trans and cis TSPN-1 dimers, respectively. In silico docking calculations partnered with our crystal structures support the importance of arginine residues in positions 29, 42 and 77 in binding sulfate groups of the dp8 and dp10 forms of heparin. The ability of several TSPN-1 domains to bind to glycosaminoglycans simultaneously probably increases the affinity of binding through multivalent interactions. The formation of cis and trans dimers of the TSPN-1 domain with relatively short segments of heparin further enhance the ability of TSP-1 to participate in high affinity binding to glycosaminoglycans. Dimer formation may also involve TSPN-1 domains from two separate TSP-1 molecules. This association would enable glycosaminoglycans to cluster TSP-1.



	Figure 2. FIGURE 2. Docked structure of dp10 heparin in complex with TSPN-1. A, TSPN-1·dp10 low energy complex identified using AutoDock4. TSPN-1 residues involved in the hydrogen bonding network are rendered in ball-and-stick. Each residue involved in the hydrogen bonding network is annotated. For clarity hydrogen bonds are not displayed. Each domain is labeled and rendered as a ribbon drawing, with -helices colored green (domain A) or magenta (domain B), and β-strands and random coil are colored cyan (domain A) or yellow (domain B). The heparin moiety dp10 is rendered in ball and stick representation. B, Molcad surface of the TSPN-1·dp10 complex with residues involved in the hydrogen bonding network colored in blue. This view of the TSPN-1·dp10 complex is the result of rotating the complex –90° around the x-axis (out of the plane of the page or screen) to provide a view of this complex from the heparin binding site, which is located at the base of complex in panel A. Figs. 2B and 4B were prepared using the SYBYL suite of programs (Tripos).		Figure 5. FIGURE 5. The native TSPN-1 structure in P1 space group. A, a ribbon drawing of the two TSPN-1 domains in one asymmetric unit. They are not related by any pseudo-symmetric operation. Residue Arg-42 from the major heparin-binding site of each domain is drawn in ball-and-stick form. The two TSPN-1 domains interact with each other extensively through their edge strands (see "Results"). The electric dipole moment of the two TSPN-1 domains is shown by the blue arrow and centered at the beginning of the arrow. B, an electrostatic potential surface representation of the two TSPN-1 domains in the native TSPN-1 structure. Residue Arg-42 from the major heparin-binding site of each TSPN-1 domain is labeled to show the separation of the two major heparin-binding sites in this native structure. The orientation of the figure is similar to the one shown in panel A.

PROCHECK

	Headers