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PDBsum entry 1nrs

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Hydrolase/hydrolase inhibitor PDB id
1nrs
Jmol
Contents
Protein chains
27 a.a. *
252 a.a. *
Ligands
LEU-ASP-PRO-ARG
ASP-PHE-GLU-GLU-
ILE-PRO-GLU-GLU-
TYS
Waters ×210
* Residue conservation analysis
PDB id:
1nrs
Name: Hydrolase/hydrolase inhibitor
Title: Crystallographic structures of thrombin complexed with throm receptor peptides: existence of expected and novel binding
Structure: Alpha-thrombin (small subunit). Chain: l. Engineered: yes. Alpha-thrombin (large subunit). Chain: h. Engineered: yes. Receptor based peptide nrp. Chain: r. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Hirudo medicinalis. Medicinal leech. Organism_taxid: 6421
Biol. unit: Tetramer (from PQS)
Resolution:
2.40Å     R-factor:   0.146    
Authors: A.Tulinsky,I.I.Mathews
Key ref:
I.I.Mathews et al. (1994). Crystallographic structures of thrombin complexed with thrombin receptor peptides: existence of expected and novel binding modes. Biochemistry, 33, 3266-3279. PubMed id: 8136362 DOI: 10.1021/bi00177a018
Date:
18-Jan-94     Release date:   31-May-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin
Seq:
Struc:
 
Seq:
Struc:
622 a.a.
27 a.a.
Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin
Seq:
Struc:
 
Seq:
Struc:
622 a.a.
252 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains L, H: E.C.3.4.21.5  - Thrombin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     blood coagulation   2 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
DOI no: 10.1021/bi00177a018 Biochemistry 33:3266-3279 (1994)
PubMed id: 8136362  
 
 
Crystallographic structures of thrombin complexed with thrombin receptor peptides: existence of expected and novel binding modes.
I.I.Mathews, K.P.Padmanabhan, V.Ganesh, A.Tulinsky, M.Ishii, J.Chen, C.W.Turck, S.R.Coughlin, J.W.Fenton.
 
  ABSTRACT  
 
Many of the vital actions of thrombin on platelets and other cells appear to be mediated by the recently cloned seven-transmembrane-domain thrombin receptor. Thrombin activates this receptor by a novel proteolytic mechanism. The amino-terminal exodomain of the receptor contains the sequence LDPRSFLLRNPNDKYEPF. Structure-activity studies with mutant receptors and receptor peptides suggest that this sequence binds to thrombin at two sites: LDPR with the active center of thrombin and KYEPF with the fibrinogen recognition exosite of thrombin. Thrombin then cleaves the Arg41-Ser42 bond to unmask a new amino terminus, which functions as a tethered peptide ligand binding to as yet undefined sites within the body of the receptor to effect receptor activation. We have determined eight crystal structures of thrombin complexed with receptor-based peptides. Each of the two components of the bidentate docking model was captured in individual cocrystals. In one crystal type, the LDPR sequence docked in the active center of thrombin in a manner analogous to d-PheProArg chloromethyl ketone. In other crystals, the KYEPF sequence bound in the fibrinogen anion binding exosite of thrombin in a manner analogous to the DFEEI sequence of the carboxylate-terminal peptide of hirudin. Strikingly, however, generation of a single crystal that includes both components of the anticipated bidentate binding mode was not achieved, apparently because the peptides have a dominant solution S-like conformation that does not bind in a productive way at the active center. This peptide structure apparently favored a novel alternative mode of receptor peptide-thrombin interaction in which the receptor peptides formed an intermolecular bridge between neighboring thrombin molecules, resulting in an infinite peptide thrombin chain in crystals. In this structure, the KYEPF sequence docked in the expected manner at the exosite of one thrombin molecule, but the LDPR sequence docked in an unusual nonproductive mode with the active center of a neighboring molecule. Mutations that removed important determinants of the S-like receptor peptide structure underlying the bridging mode in the receptor itself did not significantly alter thrombin signaling. Additionally, a comparison of receptor density to the responsiveness of a cell did not support a role for receptor oligomerization in signaling. The physiological role for this unexpected intermolecular binding mode, if any, remains to be identified.(ABSTRACT TRUNCATED AT 400 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23222541 C.Zhang, Y.Srinivasan, D.H.Arlow, J.J.Fung, D.Palmer, Y.Zheng, H.F.Green, A.Pandey, R.O.Dror, D.E.Shaw, W.I.Weis, S.R.Coughlin, and B.K.Kobilka (2012).
High-resolution crystal structure of human protease-activated receptor 1.
  Nature, 492, 387-392.
PDB code: 3vw7
20887194 C.T.Esmon, and N.L.Esmon (2011).
The link between vascular features and thrombosis.
  Annu Rev Physiol, 73, 503-514.  
20218626 M.A.Jadhav, G.Isetti, T.A.Trumbo, and M.C.Maurer (2010).
Effects of introducing fibrinogen Aalpha character into the factor XIII activation peptide segment.
  Biochemistry, 49, 2918-2924.  
19591434 T.M.Sabo, and M.C.Maurer (2009).
Biophysical investigation of GpIbalpha binding to thrombin anion binding exosite II.
  Biochemistry, 48, 7110-7122.  
18329094 E.Di Cera (2008).
Thrombin.
  Mol Aspects Med, 29, 203-254.  
18250335 P.S.Gandhi, Z.Chen, F.S.Mathews, and E.Di Cera (2008).
Structural identification of the pathway of long-range communication in an allosteric enzyme.
  Proc Natl Acad Sci U S A, 105, 1832-1837.
PDB codes: 3bef 3bei
18779330 S.Lancellotti, S.Rutella, V.De Filippis, N.Pozzi, B.Rocca, and R.De Cristofaro (2008).
Fibrinogen-elongated {gamma} Chain Inhibits Thrombin-induced Platelet Response, Hindering the Interaction with Different Receptors.
  J Biol Chem, 283, 30193-30204.  
17606903 A.Bah, Z.Chen, L.A.Bush-Pelc, F.S.Mathews, and E.Di Cera (2007).
Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4.
  Proc Natl Acad Sci U S A, 104, 11603-11608.
PDB codes: 2pux 2pv9
17347701 E.Di Cera, M.J.Page, A.Bah, L.A.Bush-Pelc, and L.C.Garvey (2007).
Thrombin allostery.
  Phys Chem Chem Phys, 9, 1291-1306.  
17635727 E.Di Cera (2007).
Thrombin as procoagulant and anticoagulant.
  J Thromb Haemost, 5, 196-202.  
17595115 M.T.Nieman, and A.H.Schmaier (2007).
Interaction of thrombin with PAR1 and PAR4 at the thrombin cleavage site.
  Biochemistry, 46, 8603-8610.  
16102053 J.A.Huntington (2005).
Molecular recognition mechanisms of thrombin.
  J Thromb Haemost, 3, 1861-1872.  
16102047 S.R.Coughlin (2005).
Protease-activated receptors in hemostasis, thrombosis and vascular biology.
  J Thromb Haemost, 3, 1800-1814.  
15152000 A.O.Pineda, C.J.Carrell, L.A.Bush, S.Prasad, S.Caccia, Z.W.Chen, F.S.Mathews, and E.Di Cera (2004).
Molecular dissection of Na+ binding to thrombin.
  J Biol Chem, 279, 31842-31853.
PDB codes: 1sfq 1sg8 1sgi 1shh
15049836 G.Isetti, and M.C.Maurer (2004).
Probing thrombin's ability to accommodate a V34F substitution within the factor XIII activation peptide segment (28-41).
  J Pept Res, 63, 241-252.  
12939269 P.J.Anderson, A.Nesset, and P.E.Bock (2003).
Effects of activation peptide bond cleavage and fragment 2 interactions on the pathway of exosite I expression during activation of human prethrombin 1 to thrombin.
  J Biol Chem, 278, 44482-44488.  
12871549 R.S.Lovely, M.Moaddel, and D.H.Farrell (2003).
Fibrinogen gamma' chain binds thrombin exosite II.
  J Thromb Haemost, 1, 124-131.  
11925440 E.P.Bianchini, V.B.Louvain, P.E.Marque, M.A.Juliano, L.Juliano, and B.F.Le Bonniec (2002).
Mapping of the catalytic groove preferences of factor Xa reveals an inadequate selectivity for its macromolecule substrates.
  J Biol Chem, 277, 20527-20534.  
12858541 S.R.Coughlin (2002).
Protease-activated receptors in the cardiovascular system.
  Cold Spring Harb Symp Quant Biol, 67, 197-208.  
11901150 T.Rose, and E.Di Cera (2002).
Three-dimensional modeling of thrombin-fibrinogen interaction.
  J Biol Chem, 277, 18875-18880.  
11925426 T.Rose, and E.Di Cera (2002).
Substrate recognition drives the evolution of serine proteases.
  J Biol Chem, 277, 19243-19246.  
11121104 T.Myles, B.F.Le Bonniec, and S.R.Stone (2001).
The dual role of thrombin's anion-binding exosite-I in the recognition and cleavage of the protease-activated receptor 1.
  Eur J Biochem, 268, 70-77.  
11562940 Y.M.Ayala, A.M.Cantwell, T.Rose, L.A.Bush, D.Arosio, and E.Di Cera (2001).
Molecular mapping of thrombin-receptor interactions.
  Proteins, 45, 107-116.  
10625611 P.E.Marque, R.Spuntarelli, L.Juliano, M.Aiach, and B.F.Le Bonniec (2000).
The role of Glu(192) in the allosteric control of the S(2)' and S(3)' subsites of thrombin.
  J Biol Chem, 275, 809-816.  
10713516 R.Krishnan, I.Mochalkin, R.Arni, and A.Tulinsky (2000).
Structure of thrombin complexed with selective non-electrophilic inhibitors having cyclohexyl moieties at P1.
  Acta Crystallogr D Biol Crystallogr, 56, 294-303.
PDB codes: 1c4u 1c4v 1c4y 1d6w 1d9i
10380350 A.Lombardi, G.De Simone, S.Galdiero, N.Staiano, F.Nastri, and V.Pavone (1999).
From natural to synthetic multisite thrombin inhibitors.
  Biopolymers, 51, 19-39.  
9873039 K.L.Hayes, and P.B.Tracy (1999).
The platelet high affinity binding site for thrombin mimics hirudin, modulates thrombin-induced platelet activation, and is distinct from the glycoprotein Ib-IX-V complex.
  J Biol Chem, 274, 972-980.  
10079109 M.L.Kahn, M.Nakanishi-Matsui, M.J.Shapiro, H.Ishihara, and S.R.Coughlin (1999).
Protease-activated receptors 1 and 4 mediate activation of human platelets by thrombin.
  J Clin Invest, 103, 879-887.  
10500117 S.R.Coughlin (1999).
How the protease thrombin talks to cells.
  Proc Natl Acad Sci U S A, 96, 11023-11027.  
  9521099 G.De Simone, A.Lombardi, S.Galdiero, F.Nastri, R.Della Morte, N.Staiano, C.Pedone, M.Bolognesi, and V.Pavone (1998).
Hirunorms are true hirudin mimetics. The crystal structure of human alpha-thrombin-hirunorm V complex.
  Protein Sci, 7, 243-253.
PDB code: 5gds
9724521 R.Krishnan, E.Zhang, K.Hakansson, R.K.Arni, A.Tulinsky, M.S.Lim-Wilby, O.E.Levy, J.E.Semple, and T.K.Brunck (1998).
Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes.
  Biochemistry, 37, 12094-12103.
PDB codes: 1ba8 1bb0 1ca8 1yyy 1zzz
  9792427 S.Tada, and J.J.Blow (1998).
The replication licensing system.
  Biol Chem, 379, 941-949.  
9618465 W.F.Xu, H.Andersen, T.E.Whitmore, S.R.Presnell, D.P.Yee, A.Ching, T.Gilbert, E.W.Davie, and D.C.Foster (1998).
Cloning and characterization of human protease-activated receptor 4.
  Proc Natl Acad Sci U S A, 95, 6642-6646.  
9342325 P.Fuentes-Prior, C.Noeske-Jungblut, P.Donner, W.D.Schleuning, R.Huber, and W.Bode (1997).
Structure of the thrombin complex with triabin, a lipocalin-like exosite-binding inhibitor derived from a triatomine bug.
  Proc Natl Acad Sci U S A, 94, 11845-11850.
PDB code: 1avg
9220985 X.He, J.Ye, C.T.Esmon, and A.R.Rezaie (1997).
Influence of Arginines 93, 97, and 101 of thrombin to its functional specificity.
  Biochemistry, 36, 8969-8976.  
8679538 B.F.Le Bonniec, T.Myles, T.Johnson, C.G.Knight, C.Tapparelli, and S.R.Stone (1996).
Characterization of the P2' and P3' specificities of thrombin using fluorescence-quenched substrates and mapping of the subsites by mutagenesis.
  Biochemistry, 35, 7114-7122.  
8913620 J.H.Matthews, R.Krishnan, M.J.Costanzo, B.E.Maryanoff, and A.Tulinsky (1996).
Crystal structures of thrombin with thiazole-containing inhibitors: probes of the S1' binding site.
  Biophys J, 71, 2830-2839.
PDB codes: 1a4w 1tbz
8702860 J.Voorberg, G.van Stempvoort, J.M.Bos, K.Mertens, J.A.van Mourik, and M.J.Donath (1996).
Enhanced thrombin sensitivity of a factor VIII-heparin cofactor II hybrid.
  J Biol Chem, 271, 20985-20988.  
8786410 P.D.Grootenhuis, and M.Karplus (1996).
Functionality map analysis of the active site cleft of human thrombin.
  J Comput Aided Mol Des, 10, 1.  
  8868478 R.Krishnan, A.Tulinsky, G.P.Vlasuk, D.Pearson, P.Vallar, P.Bergum, T.K.Brunck, and W.C.Ripka (1996).
Synthesis, structure, and structure-activity relationships of divalent thrombin inhibitors containing an alpha-keto-amide transition-state mimetic.
  Protein Sci, 5, 422-433.
PDB code: 1dit
  8732754 V.Ganesh, A.Y.Lee, J.Clardy, and A.Tulinsky (1996).
Comparison of the structures of the cyclotheonamide A complexes of human alpha-thrombin and bovine beta-trypsin.
  Protein Sci, 5, 825-835.  
  7489704 A.van de Locht, D.Lamba, M.Bauer, R.Huber, T.Friedrich, B.Kröger, W.Höffken, and W.Bode (1995).
Two heads are better than one: crystal structure of the insect derived double domain Kazal inhibitor rhodniin in complex with thrombin.
  EMBO J, 14, 5149-5157.
PDB codes: 1tbq 1tbr
7673182 E.Di Cera, E.R.Guinto, A.Vindigni, Q.D.Dang, Y.M.Ayala, M.Wuyi, and A.Tulinsky (1995).
The Na+ binding site of thrombin.
  J Biol Chem, 270, 22089-22092.  
7559498 J.Chen, H.S.Bernstein, M.Chen, L.Wang, M.Ishii, C.W.Turck, and S.R.Coughlin (1995).
Tethered ligand library for discovery of peptide agonists.
  J Biol Chem, 270, 23398-23401.  
7608215 K.Ishii, R.Gerszten, Y.W.Zheng, J.B.Welsh, C.W.Turck, and S.R.Coughlin (1995).
Determinants of thrombin receptor cleavage. Receptor domains involved, specificity, and role of the P3 aspartate.
  J Biol Chem, 270, 16435-16440.  
7744076 M.C.Bouton, J.L.Plantier, M.Dembak, M.C.Guillin, M.J.Rabiet, and M.Jandrot-Perrus (1995).
Role of the thrombin insertion loop 144-155. Study of thrombin mutations W148G, K154E and a thrombin-based synthetic peptide.
  Eur J Biochem, 229, 526-532.  
7878739 M.T.Stubbs, and W.Bode (1995).
The clot thickens: clues provided by thrombin structure.
  Trends Biochem Sci, 20, 23-28.  
7665575 T.Nanevicz, M.Ishii, L.Wang, M.Chen, J.Chen, C.W.Turck, F.E.Cohen, and S.R.Coughlin (1995).
Mechanisms of thrombin receptor agonist specificity. Chimeric receptors and complementary mutations identify an agonist recognition site.
  J Biol Chem, 270, 21619-21625.  
  7756983 J.Vijayalakshmi, K.P.Padmanabhan, K.G.Mann, and A.Tulinsky (1994).
The isomorphous structures of prethrombin2, hirugen-, and PPACK-thrombin: changes accompanying activation and exosite binding to thrombin.
  Protein Sci, 3, 2254-2271.
PDB codes: 1hag 1hah 1hai
7712286 M.T.Stubbs, and W.Bode (1994).
Coagulation factors and their inhibitors.
  Curr Opin Struct Biol, 4, 823-832.  
7937741 S.R.Coughlin (1994).
Protease-activated receptors start a family.
  Proc Natl Acad Sci U S A, 91, 9200-9202.  
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.