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PDBsum entry 2rhp

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protein ligands metals links
Cell adhesion PDB id
2rhp
Jmol PyMol
Contents
Protein chain
622 a.a. *
Ligands
NAG ×2
NAG-NAG
Metals
_CA ×30
Waters ×71
* Residue conservation analysis
PDB id:
2rhp
Name: Cell adhesion
Title: The thrombospondin-1 polymorphism asn700ser associated with artery disease causes local and long-ranging changes in pro structure
Structure: Thrombospondin-2. Chain: a. Fragment: signature domain. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Gene: thbs2, tsp2. Expressed in: spodoptera frugiperda.
Resolution:
2.90Å     R-factor:   0.229     R-free:   0.277
Authors: C.B.Carlson,J.L.Keck,D.F.Mosher
Key ref:
C.B.Carlson et al. (2008). Influences of the N700S thrombospondin-1 polymorphism on protein structure and stability. J Biol Chem, 283, 20069-20076. PubMed id: 18499674 DOI: 10.1074/jbc.M800223200
Date:
09-Oct-07     Release date:   27-May-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P35442  (TSP2_HUMAN) -  Thrombospondin-2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1172 a.a.
622 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     cell adhesion   2 terms 
  Biochemical function     calcium ion binding     2 terms  

 

 
DOI no: 10.1074/jbc.M800223200 J Biol Chem 283:20069-20076 (2008)
PubMed id: 18499674  
 
 
Influences of the N700S thrombospondin-1 polymorphism on protein structure and stability.
C.B.Carlson, Y.Liu, J.L.Keck, D.F.Mosher.
 
  ABSTRACT  
 
Thrombospondins (THBSs) are multimodular, secreted proteins characterized by a signature domain comprising a unique set of 13 calcium-binding repeats flanked by epidermal growth factor (EGF)-like and lectin-like modules. A polymorphism that changes a conserved Asn to Ser at residue 700 in the most N-terminal calcium-binding repeat of THBS-1 (repeat 1C) is found in 8-10% of European populations and has been linked to increased risk of premature coronary artery disease. The Ser substitution leads to altered stability in the EGF-like and wire modules of the THBS-1 signature domain as assessed by differential scanning calorimetry carried out in 2 mm or 200 mum calcium. Studies of the melting profiles of the THBS-2 signature domain proteins with Asn or Ser at position 702 (homologous to 700 in THBS-1) revealed that the impact of the Ser allele is similar in both THBS-1 and THBS-2. Structure determination of the Ser(702) THBS-2 variant in 2 mm calcium showed that repeat 1C contains two bound calcium ions as in the crystal of the Asn(702) protein, including the ion that is coordinated by Asn(702), and is associated with changes in conformation of repeat 1C and the adjacent EGF-like modules. The Ser substitution leads to the decreased ability of soluble THBS-2 signature domain protein to bind 4B6.13, a conformation-sensitive monoclonal antibody that recognizes an epitope in repeat 1C. These results indicate that although THBS harboring the Ser allele binds a full complement of calcium ions, repeat 1C is altered, leading to destabilization of surrounding structures.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. Overview of group A thrombospondin structure. A, modular structure of a THBS-1 or THBS-2 monomer including the N-terminal module (N), the oligomerization module (o), the von Willebrand Factor type C module (VWC), the three properdin-like modules (P1, P2, and P3), the signature domain comprising three EGF-like modules (EGF1, EGF2, and EGF3), the wire, and the lectin-like module. The signature domain is colored as follows: EGF1, yellow; EGF2, orange; EGF3, wheat; wire, blue; lectin-like module, magenta; glycosylation sites, green. Truncations of the THBS-1 signature domain used for DSC studies, EGF123-1, EGF3-wire-1, and 4C-1, are shown as above. B, crystal structure of Asn^702 THBS-2 signature domain protein and close-up stereo view of repeat 1C. Elements are colored as in above, with the addition of: water, cyan sphere; calcium ions, red spheres; Asn^702, white Corey-Pauling-Kultin (CPK) sticks; disulfide, yellow sulfur atoms. N and C termini of repeat 1C are indicated in the close-up view. Images prepared using PyMol (39). C, sequences of wire repeat 1C of THBS-1 and THBS-2. Residues conserved between THBS-1 and THBS-2 are shown in bold. The glycosylation site in the insert (Asn^708/710) is indicated by a green arrow. Black arrows indicate Trp^698/700, used as a reporter in previous biophysical studies (12, 13), and Asn^700/702, the site of the THBS-1 polymorphism associated with premature coronary artery disease. Residues critical for 4B6.13 recognition, Leu^703 and His^722, are indicated by asterisks. As determined in the Asn^702 THBS-2 signature domain structure, and suggested for THBS-1, residues involved in calcium coordination are colored as follows: bidentate side chain coordination, red; single side chain coordination, purple; main chain coordination, green; coordination via a water molecule, blue.
Figure 3.
FIGURE 3. Electron density and superposition analysis of Asn^702 and Ser^702 THBS-2 signature domain proteins. A, stereo image of 2F[o] – F[c] electron density map (contoured at 1.5 and colored blue) for Asn^702 and nearby residues. B, stereo image of 2F[o] – F[c] electron density map (contoured at 1.5 and colored blue) for Ser^702 and nearby residues. Calcium ions are shown as gray spheres and water molecules are shown as yellow spheres. Images were prepared using CCP4 Molecular Graphics (17). C and D, superpose analysis was performed on C atoms from the entire protein, residues 551–1171. C, overlay of wire repeat 1C and nearby residues. Calcium ions are shown as spheres. Asn/Ser^702 and residues responsible for the 4B6.13 epitope, Leu^703 and His^722, are shown as sticks. Asn^702 THBS-2 signature domain is shown in blue/light blue and Ser^702 THBS-2 signature domain is shown in red/pink. Wire repeat 1C is shown in blue and red. D, r.m.s. deviation analysis of the difference between the Asn^702 and Ser^702 THBS-2 signature domain main chain atoms. Large red dotted box comprises wire module residues and the small red dotted box comprises wire repeat 1C residues.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 20069-20076) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19706610 Y.Liu, and D.F.Mosher (2009).
Interactions among stalk modules of thrombospondin-1.
  J Biol Chem, 284, 28563-28570.  
19531495 Y.Liu, D.S.Annis, and D.F.Mosher (2009).
Interactions among the epidermal growth factor-like modules of thrombospondin-1.
  J Biol Chem, 284, 22206-22212.  
18682400 C.B.Carlson, K.A.Gunderson, and D.F.Mosher (2008).
Mutations targeting intermodular interfaces or calcium binding destabilize the thrombospondin-2 signature domain.
  J Biol Chem, 283, 27089-27099.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.

 

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