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PDBsum entry 1a0h
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protein ligands Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
1a0h

 

 

 

 

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Contents
Protein chains
159 a.a. *
259 a.a. *
Ligands
NAG-NAG ×2
0G6 ×2
Waters ×87
* Residue conservation analysis
PDB id:
1a0h
Name: Hydrolase/hydrolase inhibitor
Title: The x-ray crystal structure of ppack-meizothrombin desf1: kringle/thrombin and carbohydrate/kringle/thrombin interactions and location of the linker chain
Structure: Meizothrombin. Chain: a, d. Fragment: f2/thrombin domain. Synonym: desf1. Meizothrombin. Chain: b, e. Fragment: f2/thrombin domain. Synonym: desf1. Ec: 3.4.21.5
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: blood. Tissue: blood plasma. Tissue: blood plasma
Biol. unit: Hexamer (from PQS)
Resolution:
3.20Å     R-factor:   0.205     R-free:   0.242
Authors: P.D.Martin,M.G.Malkowski,J.Box,C.T.Esmon,B.F.P.Edwards
Key ref:
P.D.Martin et al. (1997). New insights into the regulation of the blood clotting cascade derived from the X-ray crystal structure of bovine meizothrombin des F1 in complex with PPACK. Structure, 5, 1681-1693. PubMed id: 9438869 DOI: 10.1016/S0969-2126(97)00314-6
Date:
30-Nov-97     Release date:   17-Jun-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00735  (THRB_BOVIN) -  Prothrombin from Bos taurus
Seq:
Struc: 		 
Seq:
Struc: 		625 a.a.
159 a.a.*
Protein chains
Pfam   ArchSchema ?
P00735  (THRB_BOVIN) -  Prothrombin from Bos taurus
Seq:
Struc: 		 
Seq:
Struc: 		625 a.a.
259 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, D, E: 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.

 

 
DOI no: 10.1016/S0969-2126(97)00314-6 Structure 5:1681-1693 (1997)
PubMed id: 9438869  
 
 
New insights into the regulation of the blood clotting cascade derived from the X-ray crystal structure of bovine meizothrombin des F1 in complex with PPACK.
P.D.Martin, M.G.Malkowski, J.Box, C.T.Esmon, B.F.Edwards.
 
  ABSTRACT  
 
BACKGROUND: The conversion of prothrombin to thrombin by factor Xa is the penultimate step in the blood clotting cascade. In vivo, where the conversion occurs primarily on activated platelets in association with factor Va and Ca2+ ions, meizothrombin is the major intermediate of the two step reaction. Meizothrombin rapidly loses the fragment 1 domain (F1) by autolysis to become meizothrombin des F1 (mzTBN-F1). The physiological properties of mzTBN-F1 differ dramatically from those of thrombin due to the presence of prothrombin fragment 2 (F2), which remains covalently attached to the activated thrombin domain in mzTBN-F1. RESULTS: The crystal structure of mzTBN-F1 has been determined at 3.1 A resolution by molecular replacement, using only the thrombin domain, and refined to R and Rfree values of 0.205 and 0.242, respectively. The protease active site was inhibited with D-Phe-Pro-Arg-chloromethylketone (PPACK) to reduce autolysis. The mobile linker chain connecting the so-called kringle and thrombin domains and the first two N-acetylglucosamine residues attached to the latter were seen in electron-density maps improved with the program SQUASH. Previously these regions had only been modeled. CONCLUSIONS: The F2 kringle domain in mzTBN-F1 is bound to the electropositive heparin-binding site on thrombin in an orientation that is systematically shifted and has significantly more interdomain contacts compared to a noncovalent complex of free F2 and free thrombin. F2 in mzTBN-F1 forms novel hydrogen bonds to the carbohydrate chain of thrombin and perhaps stabilizes a unique, rigid conformation of the gamma-autolysis loop through non-local effects. The F2 linker chain, which does not interfere with the active site or fibrinogen-recognition site, is arranged so that the two sites cleaved by factor Xa are separated by 36 A. The two mzTBN-F1 molecules in the asymmetric unit share a tight 'dimer' contact in which the active site of one molecule is partially blocked by the F2 kringle domain of its partner. This interaction suggests a new model for prothrombin organization.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The interface between the F2 kringle domain and thrombin. Residues between the thrombin (red) and F2 kringle (blue) domains that are within 5 Å of one another are shown in stereo. Hydrogen bonds are shown as dashed lines (green). For clarity, residues are identified only by their prothrombin sequence position.
 
  The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 1681-1693) copyright 1997.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19858193 H.N.Bradford, J.A.Micucci, and S.Krishnaswamy (2010).
Regulated cleavage of prothrombin by prothrombinase: repositioning a cleavage site reveals the unique kinetic behavior of the action of prothrombinase on its compound substrate.
  J Biol Chem, 285, 328-338.  
20722419 J.Hirbawi, J.L.Vaughn, M.A.Bukys, H.L.Vos, and M.Kalafatis (2010).
Contribution of Amino Acid Region 659-663 of Factor Va Heavy Chain to the Activity of Factor Xa within Prothrombinase .
  Biochemistry, 49, 8520-8534.  
18590276 J.Hirbawi, M.A.Bukys, M.A.Barhoover, E.Erdogan, and M.Kalafatis (2008).
Role of the acidic hirudin-like COOH-terminal amino acid region of factor Va heavy chain in the enhanced function of prothrombinase.
  Biochemistry, 47, 7963-7974.  
18991406 M.A.Barhoover, T.Orban, M.A.Bukys, and M.Kalafatis (2008).
Cooperative regulation of the activity of factor Xa within prothrombinase by discrete amino acid regions from factor Va heavy chain.
  Biochemistry, 47, 12835-12843.  
18854941 M.E.Papaconstantinou, P.S.Gandhi, Z.Chen, A.Bah, and E.Di Cera (2008).
Na+ binding to meizothrombin desF1.
  Cell Mol Life Sci, 65, 3688-3697.
PDB code: 3e6p
18320260 R.G.Melvin, S.D.Katewa, and J.W.Ballard (2008).
A candidate complex approach to study functional mitochondrial DNA changes: sequence variation and quaternary structure modeling of Drosophila simulans cytochrome c oxidase.
  J Mol Evol, 66, 232-242.  
18286181 S.Macedo-Ribeiro, C.Almeida, B.M.Calisto, T.Friedrich, R.Mentele, J.Stürzebecher, P.Fuentes-Prior, and P.J.Pereira (2008).
Isolation, cloning and structural characterisation of boophilin, a multifunctional Kunitz-type proteinase inhibitor from the cattle tick.
  PLoS ONE, 3, e1624.
PDB code: 2ody
17334934 S.K.Dasgupta, and P.Thiagarajan (2007).
Inhibition of thrombin activity by prothrombin activation fragment 1.2.
  J Thromb Thrombolysis, 24, 157-162.  
16537482 E.Gherardi, S.Sandin, M.V.Petoukhov, J.Finch, M.E.Youles, L.G.Ofverstedt, R.N.Miguel, T.L.Blundell, G.F.Vande Woude, U.Skoglund, and D.I.Svergun (2006).
Structural basis of hepatocyte growth factor/scatter factor and MET signalling.
  Proc Natl Acad Sci U S A, 103, 4046-4051.
PDB codes: 2ced 2cee 2ceg 2cew
17020886 M.A.Bukys, P.Y.Kim, M.E.Nesheim, and M.Kalafatis (2006).
A control switch for prothrombinase: characterization of a hirudin-like pentapeptide from the COOH terminus of factor Va heavy chain that regulates the rate and pathway for prothrombin activation.
  J Biol Chem, 281, 39194-39204.  
15897196 M.A.Bukys, M.A.Blum, P.Y.Kim, N.Brufatto, M.E.Nesheim, and M.Kalafatis (2005).
Incorporation of factor Va into prothrombinase is required for coordinated cleavage of prothrombin by factor Xa.
  J Biol Chem, 280, 27393-27401.  
15634266 S.Krishnaswamy (2005).
Exosite-driven substrate specificity and function in coagulation.
  J Thromb Haemost, 3, 54-67.  
15892855 W.Bode (2005).
The structure of thrombin, a chameleon-like proteinase.
  J Thromb Haemost, 3, 2379-2388.  
14988397 D.S.Boskovic, T.Troxler, and S.Krishnaswamy (2004).
Active site-independent recognition of substrates and product by bovine prothrombinase: a fluorescence resonance energy transfer study.
  J Biol Chem, 279, 20786-20793.  
15494418 S.J.Orcutt, and S.Krishnaswamy (2004).
Binding of substrate in two conformations to human prothrombinase drives consecutive cleavage at two sites in prothrombin.
  J Biol Chem, 279, 54927-54936.  
12814644 B.R.Lentz (2003).
Exposure of platelet membrane phosphatidylserine regulates blood coagulation.
  Prog Lipid Res, 42, 423-438.  
12496269 N.Brufatto, and M.E.Nesheim (2003).
Analysis of the kinetics of prothrombin activation and evidence that two equilibrating forms of prothrombinase are involved in the process.
  J Biol Chem, 278, 6755-6764.  
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.  
12939270 P.J.Anderson, and P.E.Bock (2003).
Role of prothrombin fragment 1 in the pathway of regulatory exosite I formation during conversion of human prothrombin to thrombin.
  J Biol Chem, 278, 44489-44495.  
11724802 I.M.Verhamme, S.T.Olson, D.M.Tollefsen, and P.E.Bock (2002).
Binding of exosite ligands to human thrombin. Re-evaluation of allosteric linkage between thrombin exosites I and II.
  J Biol Chem, 277, 6788-6798.  
11060016 J.L.Richardson, B.Kröger, W.Hoeffken, J.E.Sadler, P.Pereira, R.Huber, W.Bode, and P.Fuentes-Prior (2000).
Crystal structure of the human alpha-thrombin-haemadin complex: an exosite II-binding inhibitor.
  EMBO J, 19, 5650-5660.
PDB code: 1e0f
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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