PDBsum entry 2pf5

Cell adhesion

PDB id: 2pf5

Contents

Protein chains

88 a.a. *

94 a.a. *

96 a.a. *

85 a.a. *

Ligands

SO4 ×2

2PE ×5

Waters ×414

* Residue conservation analysis

PDB id:

2pf5

Name:

Cell adhesion

Title:

Crystal structure of the human tsg-6 link module

Structure:

Tumor necrosis factor-inducible protein tsg-6. Chain: a, b, c, d, e. Fragment: link_module, residues 36-133 in preprotein. Synonym: tnf- stimulated gene 6 protein. Hyaluronate-binding protein. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: tnfaip6, tsg6. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Other_details: see day et al. (1996) protein expression & purification 8, 1-16.

Resolution:

1.90Å R-factor: 0.196 R-free: 0.226

Authors:

V.A.Higman,D.J.Mahoney,M.E.M.Noble,A.J.Day

Key ref:

V.A.Higman et al. (2007). Plasticity of the TSG-6 HA-binding loop and mobility in the TSG-6-HA complex revealed by NMR and X-ray crystallography. J Mol Biol, 371, 669-684. PubMed id: 17585936 DOI: 10.1016/j.jmb.2007.05.073

Date:

04-Apr-07 Release date: 26-Jun-07

Protein chain

P98066  (TSG6_HUMAN) -  Tumor necrosis factor-inducible gene 6 protein from Homo sapiens

Seq: 277 a.a.

Struc: 88 a.a.

Protein chains

P98066  (TSG6_HUMAN) -  Tumor necrosis factor-inducible gene 6 protein from Homo sapiens

Seq: 277 a.a.

Struc: 94 a.a.

Protein chain

P98066  (TSG6_HUMAN) -  Tumor necrosis factor-inducible gene 6 protein from Homo sapiens

Seq: 277 a.a.

Struc: 96 a.a.

Protein chain

P98066  (TSG6_HUMAN) -  Tumor necrosis factor-inducible gene 6 protein from Homo sapiens

Seq: 277 a.a.

Struc: 85 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E: E.C.3.1.1.- - ?????

DOI no: 10.1016/j.jmb.2007.05.073

J Mol Biol 371:669-684 (2007)

PubMed id: 17585936

Plasticity of the TSG-6 HA-binding loop and mobility in the TSG-6-HA complex revealed by NMR and X-ray crystallography.

V.A.Higman, C.D.Blundell, D.J.Mahoney, C.Redfield, M.E.Noble, A.J.Day.

ABSTRACT

Tumour necrosis factor-stimulated gene-6 (TSG-6) is a glycosaminoglycan-binding protein expressed during inflammatory and inflammation-like processes. Previously NMR structures were calculated for the Link module of TSG-6 (Link_TSG6) in its free state and when bound to an octasaccharide of hyaluronan (HA(8)). Heparin was found to compete for HA binding even though it interacts at a site that is distinct from the HA-binding surface. Here we present crystallography data on the free protein, and (15)N NMR relaxation data for the uncomplexed and HA(8)-bound forms of Link_TSG6. Although the Link module is comparatively rigid overall, the free protein shows a high degree of mobility in the beta4/beta5 loop and at the Cys47-Cys68 disulfide bond, both of which are regions involved in HA binding. When bound to HA(8), this dynamic behaviour is dampened, but not eliminated, suggesting a degree of dynamic matching between the protein and sugar that may decrease the entropic penalty of complex formation. A further highly dynamic residue is Lys54, which is distant from the HA-binding site, but was previously shown to be involved in heparin binding. When HA is bound, Lys54 becomes less mobile, providing evidence for an allosteric effect linking the HA and heparin-binding sites. A mechanism is suggested involving the beta2-strand and alpha2-helix. The crystal structure of free Link_TSG6 contains five molecules in the asymmetric unit that are highly similar to the NMR structure and support the dynamic behaviour seen near the HA-binding site: they show little or no electron density for the beta4/beta5 loop and display multiple conformations for the Cys47-Cys68 disulfide bond. The crystal structures were used in docking calculations with heparin. An extended interface between a Link_TSG6 dimer and heparin 11-mer was identified that is in excellent agreement with previous mutagenesis and calorimetric data, providing the basis for further investigation of this interaction.

Selected figure(s)

Figure 1.
Figure 1. ^15N{^1H} NOE as I[sat]/I[nonsat] for free (black) and HA[8]-bound (red) Link_TSG6. Data were collected at 500 MHz. The secondary structure organisation of Link_TSG6 is indicated along the top of the graph. Also indicated is the B-factor as a function of residue for chains A (yellow), B (light green), C (cyan), D (light blue) and E (bright blue) of the crystal structure of Link_TSG6.

Figure 4.
Figure 4. (a) Superposition of chains A–E (yellow, light green, cyan, light blue, bright blue, respectively) of the crystal structure of Link_TSG6 showing the β4/β5 loop region. (b) Superposition of chains A–E of the crystal structure of Link_TSG6 as in (a) with the lowest energy NMR structures of free (magenta) and HA[8]-bound (purple) Link_TSG6. (c) and (d) are as (a) and (b), respectively, but showing the β4/β5 loop region only.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 371, 669-684) copyright 2007.

Figures were selected by the author.