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PDBsum entry 1dec
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Blood coagulation PDB id
1dec

 

 

 

 

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Contents
Protein chain
39 a.a.
PDB id:
1dec
Name: Blood coagulation
Title: Structure of the rgd protein decorsin: conserved motif and distinct function in leech proteins that affect blood clotting
Structure: Decorsin. Chain: a. Engineered: yes
Source: Macrobdella decora. North american leech. Organism_taxid: 6405. Organ: blood
NMR struc: 25 models
Authors: A.M.Krezel,G.Wagner,J.Seymour-Ulmer,R.A.Lazarus
Key ref: A.M.Krezel et al. (1994). Structure of the RGD protein decorsin: conserved motif and distinct function in leech proteins that affect blood clotting. Science, 264, 1944-1947. PubMed id: 8009227 DOI: 10.1126/science.8009227
Date:
17-May-94     Release date:   31-Aug-94    
PROCHECK
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 Headers
 References

Protein chain
P17350  (DECO_MACDE) -  Decorsin from Macrobdella decora
Seq:
Struc: 		39 a.a.
39 a.a.
Key:    Secondary structure

 

 
DOI no: 10.1126/science.8009227 Science 264:1944-1947 (1994)
PubMed id: 8009227  
 
 
Structure of the RGD protein decorsin: conserved motif and distinct function in leech proteins that affect blood clotting.
A.M.Krezel, G.Wagner, J.Seymour-Ulmer, R.A.Lazarus.
 
  ABSTRACT  
 
The structure of the leech protein decorsin, a potent 39-residue antagonist of glycoprotein IIb-IIIa and inhibitor of platelet aggregation, was determined by nuclear magnetic resonance. In contrast to other disintegrins, the Arg-Gly-Asp (RGD)-containing region of decorsin is well defined. The three-dimensional structure of decorsin is similar to that of hirudin, an anticoagulant leech protein that potently inhibits thrombin. Amino acid sequence comparisons suggest that ornatin, another glycoprotein IIb-IIIa antagonist, and antistasin, a potent Factor Xa inhibitor and anticoagulant found in leeches, share the same structural motif. Although decorsin, hirudin, and antistasin all affect the blood clotting process and appear similar in structure, their mechanisms of action and epitopes important for binding to their respective targets are distinct.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21158638 G.S.Min, I.N.Sarkar, and M.E.Siddall (2010).
Salivary transcriptome of the North American medicinal leech, Macrobdella decora.
  J Parasitol, 96, 1211-1221.  
15390258 J.H.Shiu, C.Y.Chen, L.S.Chang, Y.C.Chen, Y.C.Chen, Y.H.Lo, Y.C.Liu, and W.J.Chuang (2004).
Solution structure of gamma-bungarotoxin: the functional significance of amino acid residues flanking the RGD motif in integrin binding.
  Proteins, 57, 839-849.
PDB code: 1mr6
14579362 C.Micheletti, V.De Filippis, A.Maritan, and F.Seno (2003).
Elucidation of the disulfide-folding pathway of hirudin by a topology-based approach.
  Proteins, 53, 720-730.  
11877740 H.S.Park, C.Kim, and Y.K.Kang (2002).
Preferred conformations of RGDX tetrapeptides to inhibit the binding of fibrinogen to platelets.
  Biopolymers, 63, 298-313.  
11327857 N.Assa-Munt, X.Jia, P.Laakkonen, and E.Ruoslahti (2001).
Solution structures and integrin binding activities of an RGD peptide with two isomers.
  Biochemistry, 40, 2373-2378.
PDB codes: 1ful 1fuv
  10975565 A.M.Krezel, J.S.Ulmer, G.Wagner, and R.A.Lazarus (2000).
Recombinant decorsin: dynamics of the RGD recognition site.
  Protein Sci, 9, 1428-1438.  
10504384 B.M.Duggan, H.J.Dyson, and P.E.Wright (1999).
Inherent flexibility in a potent inhibitor of blood coagulation, recombinant nematode anticoagulant protein c2.
  Eur J Biochem, 265, 539-548.
PDB code: 1cou
10103011 E.Kellenberger, G.Mer, C.Kellenberger, G.Marguerie, and J.F.Lefèvre (1999).
Solution structure of a conformationally constrained Arg-Gly-Asp-like motif inserted into the alpha/beta scaffold of leiurotoxin I.
  Eur J Biochem, 260, 810-817.  
10563507 F.Vella, J.F.Hernandez, A.Molla, M.R.Block, and G.J.Arlaud (1999).
Grafting an RGD motif onto an epidermal growth factor-like module: chemical synthesis and functional characterization of the chimeric molecule.
  J Pept Res, 54, 415-426.  
  9420281 N.Verdaguer, N.Sevilla, M.L.Valero, D.Stuart, E.Brocchi, D.Andreu, E.Giralt, E.Domingo, M.G.Mateu, and I.Fita (1998).
A similar pattern of interaction for different antibodies with a major antigenic site of foot-and-mouth disease virus: implications for intratypic antigenic variation.
  J Virol, 72, 739-748.  
  9521121 P.Polverino de Laureto, E.Scaramella, V.De Filippis, O.Marin, M.G.Doni, and A.Fontana (1998).
Chemical synthesis and structural characterization of the RGD-protein decorsin: a potent inhibitor of platelet aggregation.
  Protein Sci, 7, 433-444.  
9442878 D.J.Leahy (1997).
Implications of atomic-resolution structures for cell adhesion.
  Annu Rev Cell Dev Biol, 13, 363-393.  
9343347 E.Domingo, and J.J.Holland (1997).
RNA virus mutations and fitness for survival.
  Annu Rev Microbiol, 51, 151-178.  
9258751 J.T.Stubbs, K.P.Mintz, E.D.Eanes, D.A.Torchia, and L.W.Fisher (1997).
Characterization of native and recombinant bone sialoprotein: delineation of the mineral-binding and cell adhesion domains and structural analysis of the RGD domain.
  J Bone Miner Res, 12, 1210-1222.  
9260929 M.R.Taylor, J.R.Couto, C.D.Scallan, R.L.Ceriani, and J.A.Peterson (1997).
Lactadherin (formerly BA46), a membrane-associated glycoprotein expressed in human milk and breast carcinomas, promotes Arg-Gly-Asp (RGD)-dependent cell adhesion.
  DNA Cell Biol, 16, 861-869.  
9150463 M.S.Goligorsky, E.Noiri, H.Kessler, and V.Romanov (1997).
Therapeutic potential of RGD peptides in acute renal injury.
  Kidney Int, 51, 1487-1492.  
9268674 P.Lanza, B.Felding-Habermann, Z.M.Ruggeri, M.Zanetti, and R.Billetta (1997).
Selective interaction of a conformationally-constrained Arg-Gly-Asp (RGD) motif with the integrin receptor alphavbeta3 expressed on human tumor cells.
  Blood Cells Mol Dis, 23, 230-241.  
9032072 P.R.Mittl, S.Di Marco, G.Fendrich, G.Pohlig, J.Heim, C.Sommerhoff, H.Fritz, J.P.Priestle, and M.G.Grütter (1997).
A new structural class of serine protease inhibitors revealed by the structure of the hirustasin-kallikrein complex.
  Structure, 5, 253-264.
PDB code: 1hia
9311976 R.Lapatto, U.Krengel, H.A.Schreuder, A.Arkema, B.de Boer, K.H.Kalk, W.G.Hol, P.D.Grootenhuis, J.W.Mulders, R.Dijkema, H.J.Theunissen, and B.W.Dijkstra (1997).
X-ray structure of antistasin at 1.9 A resolution and its modelled complex with blood coagulation factor Xa.
  EMBO J, 16, 5151-5161.
PDB code: 1skz
9012916 A.Eldor, M.Orevi, and M.Rigbi (1996).
The role of the leech in medical therapeutics.
  Blood Rev, 10, 201-209.  
8548820 D.J.Leahy, I.Aukhil, and H.P.Erickson (1996).
2.0 A crystal structure of a four-domain segment of human fibronectin encompassing the RGD loop and synergy region.
  Cell, 84, 155-164.
PDB code: 1fnf
8637900 J.I.Jones, T.Prevette, A.Gockerman, and D.R.Clemmons (1996).
Ligand occupancy of the alpha-V-beta3 integrin is necessary for smooth muscle cells to migrate in response to insulin-like growth factor.
  Proc Natl Acad Sci U S A, 93, 2482-2487.  
8639264 J.R.Couto, M.R.Taylor, S.G.Godwin, R.L.Ceriani, and J.A.Peterson (1996).
Cloning and sequence analysis of human breast epithelial antigen BA46 reveals an RGD cell adhesion sequence presented on an epidermal growth factor-like domain.
  DNA Cell Biol, 15, 281-286.  
8688423 O.Lequin, C.Albaret, F.Bontems, G.Spik, and J.Y.Lallemand (1996).
Solution structure of bovine angiogenin by 1H nuclear magnetic resonance spectroscopy.
  Biochemistry, 35, 8870-8880.
PDB code: 1gio
8922391 R.A.Lue, E.Brandin, E.P.Chan, and D.Branton (1996).
Two independent domains of hDlg are sufficient for subcellular targeting: the PDZ1-2 conformational unit and an alternatively spliced domain.
  J Cell Biol, 135, 1125-1137.  
7568238 A.Kidera (1995).
Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide.
  Proc Natl Acad Sci U S A, 92, 9886-9889.  
8846226 B.Zhao, L.R.Helms, R.L.DesJarlais, S.S.Abdel-Meguid, and R.Wetzel (1995).
A paradigm for drug discovery using a conformation from the crystal structure of a presentation scaffold.
  Nat Struct Biol, 2, 1131-1137.  
8828146 E.Domingo, M.G.Mateu, C.Escarmís, E.Martínez-Salas, D.Andreu, E.Giralt, N.Verdaguer, and I.Fita (1995).
Molecular evolution of aphthoviruses.
  Virus Genes, 11, 197-207.  
  7537661 N.Verdaguer, M.G.Mateu, D.Andreu, E.Giralt, E.Domingo, and I.Fita (1995).
Structure of the major antigenic loop of foot-and-mouth disease virus complexed with a neutralizing antibody: direct involvement of the Arg-Gly-Asp motif in the interaction.
  EMBO J, 14, 1690-1696.  
8569452 P.Ascenzi, G.Amiconi, W.Bode, M.Bolognesi, M.Coletta, and E.Menegatti (1995).
Proteinase inhibitors from the European medicinal leech Hirudo medicinalis: structural, functional and biomedical aspects.
  Mol Aspects Med, 16, 215-313.  
8591029 P.Zhang, S.Talluri, H.Deng, D.Branton, and G.Wagner (1995).
Solution structure of the pleckstrin homology domain of Drosophila beta-spectrin.
  Structure, 3, 1185-1195.
PDB code: 1dro
7634091 M.J.Sutcliffe, M.Jaseja, E.I.Hyde, X.Lu, and J.A.Williams (1994).
Three-dimensional structure of the RGD-containing neurotoxin homologue dendroaspin.
  Nat Struct Biol, 1, 802-807.
PDB code: 1drs
7813476 M.Jaseja, X.Lu, J.A.Williams, M.J.Sutcliffe, V.V.Kakkar, R.A.Parslow, and E.I.Hyde (1994).
1H-NMR assignments and secondary structure of dendroaspin, an RGD-containing glycoprotein IIb-IIIa (alpha IIb-beta 3) antagonist with a neurotoxin fold.
  Eur J Biochem, 226, 861-868.  
7712286 M.T.Stubbs, and W.Bode (1994).
Coagulation factors and their inhibitors.
  Curr Opin Struct Biol, 4, 823-832.  
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. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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