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PDBsum entry 1a5h
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Hydrolase PDB id
1a5h

 

 

 

 

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Contents
Protein chain
252 a.a. *
Ligands
THR-CYS-GLY-LEU-
ARG-GLN-TYR ×2
BBA ×2
Waters ×273
* Residue conservation analysis
PDB id:
1a5h
Name: Hydrolase
Title: Catalytic domain of human two-chain tissue plasminogen activator complex of a bis-benzamidine
Structure: Tissue plasminogen activator. Chain: c, d. Fragment: heavy chain fragment, catalytic domain. Engineered: yes. Tissue plasminogen activator. Chain: a, b. Fragment: light chain, catalytic domain. Synonym: tc-tpa(bisb). Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.90Å     R-factor:   0.178    
Authors: M.Renatus,W.Bode,M.T.Stubbs
Key ref:
M.Renatus et al. (1997). Structural mapping of the active site specificity determinants of human tissue-type plasminogen activator. Implications for the design of low molecular weight substrates and inhibitors. J Biol Chem, 272, 21713-21719. PubMed id: 9268299 DOI: 10.1074/jbc.272.35.21713
Date:
17-Feb-98     Release date:   20-Apr-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P00750  (TPA_HUMAN) -  Tissue-type plasminogen activator from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		562 a.a.
252 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.68  - t-plasminogen activator.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Specific cleavage of Arg-|-Val bond in plasminogen to form plasmin.

 

 
DOI no: 10.1074/jbc.272.35.21713 J Biol Chem 272:21713-21719 (1997)
PubMed id: 9268299  
 
 
Structural mapping of the active site specificity determinants of human tissue-type plasminogen activator. Implications for the design of low molecular weight substrates and inhibitors.
M.Renatus, W.Bode, R.Huber, J.Stürzebecher, D.Prasa, S.Fischer, U.Kohnert, M.T.Stubbs.
 
  ABSTRACT  
 
The recent structure determination of the catalytic domain of tissue-type plasminogen activator (tPA) suggested residue Arg174 could play a role in P3/P4 substrate specificity. Six synthetic chromogenic tPA substrates of the type R-Xaa-Gly-Arg-p-nitroanilide, in which R is an N-terminal protection group, were synthesized to test this property. Although changing the residue Xaa (in its L or D form) at position P3 from the hydrophobic Phe to an acidic residue, Asp or Glu, gave no improvement in catalytic efficiency, comparative analysis of the substrates indicated a preference for an acidic substituent occupying the S3 site when the S4 site contains a hydrophobic or basic moiety. The 2.9 A structure determination of the catalytic domain of human tPA in complex with the bis-benzamidine inhibitor 2, 7-bis-(4-amidinobenzylidene)-cycloheptan-1-one reveals a three-site interaction, salt bridge formation of the proximal amidino group of the inhibitor with Asp189 in the primary specificity pocket, extensive hydrophobic surface burial, and a weak electrostatic interaction between the distal amidino group of the inhibitor and two carbonyl oxygens of the protein. The latter position was previously occupied by the guanidino group of Arg174, which swings out to form the western edge of the S3 pocket. These data suggest that the side chain of Arg174 is flexible, and does not play a major role in the S4 specificity of tPA. On the other hand, this residue would modulate S3 specificity, and may be exploited to fine tune the specificity and selectivity of tPA substrates and inhibitors.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Experimental density (2F[o] F[c]) for the 186-loop of tPA, showing the cluster of Arg186A, Gln186C, His188. Gly19 of the activation peptide is adjacent to this loop (lower right), as is the strand His159-Arg161 (bottom). Orientation as in Fig. 1. 		Figure 4.
Fig. 4. Active site region of human tPA in complex with the bis-benzamidine inhibitor. The proximal benzamidine occupies the^ specificity pocket, and the distal benzamidine reaches toward^ an electrophilic pocket formed by the side chain carbonyl atoms of Asp97, Thr98, and Arg174. The benzyl ring of the inhibitor is perpendicular to the side^ chain of Tyr99; the side chain of Arg174 is displaced by the amidino group. A, experimental density (2F[o] F[c]) of the active site region in complex with the bis-benzamidine^ inhibitor. B, active site region of human tPA in complex with bis-benzamidine. Arg174 from b-tPA is superimposed (thin lines).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1997, 272, 21713-21719) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20087367 H.N.David, B.Haelewyn, J.J.Risso, N.Colloc'h, and J.H.Abraini (2010).
Xenon is an inhibitor of tissue-plasminogen activator: adverse and beneficial effects in a rat model of thromboembolic stroke.
  J Cereb Blood Flow Metab, 30, 718-728.  
19435349 X.Li, X.He, B.Wang, and K.Merz (2009).
Conformational variability of benzamidinium-based inhibitors.
  J Am Chem Soc, 131, 7742-7754.  
15861134 M.G.Medina, M.D.Ledesma, J.E.Domínguez, M.Medina, D.Zafra, F.Alameda, C.G.Dotti, and P.Navarro (2005).
Tissue plasminogen activator mediates amyloid-induced neurotoxicity via Erk1/2 activation.
  EMBO J, 24, 1706-1716.  
12437122 D.Rauh, S.Reyda, G.Klebe, and M.T.Stubbs (2002).
Trypsin mutants for structure-based drug design: expression, refolding and crystallisation.
  Biol Chem, 383, 1309-1314.  
11928826 E.Anglés-Cano, and G.Rojas (2002).
Apolipoprotein(a): structure-function relationship at the lysine-binding site and plasminogen activator cleavage site.
  Biol Chem, 383, 93-99.  
11080640 R.Tranter, J.A.Read, R.Jones, and R.L.Brady (2000).
Effector sites in the three-dimensional structure of mammalian sperm beta-acrosin.
  Structure, 8, 1179-1188.
PDB codes: 1fiw 1fiz
10801494 V.L.Nienaber, D.Davidson, R.Edalji, V.L.Giranda, V.Klinghofer, J.Henkin, P.Magdalinos, R.Mantei, S.Merrick, J.M.Severin, R.A.Smith, K.Stewart, K.Walter, J.Wang, M.Wendt, M.Weitzberg, X.Zhao, and T.Rockway (2000).
Structure-directed discovery of potent non-peptidic inhibitors of human urokinase that access a novel binding subsite.
  Structure, 8, 553-563.  
10102985 H.Czapinska, and J.Otlewski (1999).
Structural and energetic determinants of the S1-site specificity in serine proteases.
  Eur J Biochem, 260, 571-595.  
10556566 L.Hervio, C.Brunner, L.Sorell, C.Kang, H.Müller, and E.Anglés-Cano (1999).
Effect of plasminogen activators on human recombinant apolipoprotein(a) having the plasminogen activation cleavage site.
  Biochim Biophys Acta, 1434, 124-134.  
9753698 M.A.Parry, U.Jacob, R.Huber, A.Wisner, C.Bon, and W.Bode (1998).
The crystal structure of the novel snake venom plasminogen activator TSV-PA: a prototype structure for snake venom serine proteinases.
  Structure, 6, 1195-1206.
PDB code: 1bqy
  9524060 M.T.Stubbs, M.Renatus, and W.Bode (1998).
An active zymogen: unravelling the mystery of tissue-type plasminogen activator.
  Biol Chem, 379, 95.  
9354616 M.Renatus, M.T.Stubbs, R.Huber, P.Bringmann, P.Donner, W.D.Schleuning, and W.Bode (1997).
Catalytic domain structure of vampire bat plasminogen activator: a molecular paradigm for proteolysis without activation cleavage.
  Biochemistry, 36, 13483-13493.
PDB code: 1a5i
9434908 W.Bode, and M.Renatus (1997).
Tissue-type plasminogen activator: variants and crystal/solution structures demarcate structural determinants of function.
  Curr Opin Struct Biol, 7, 865-872.  
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 codes are shown on the right.

 

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