PDBsum entry 1c9p

Go to PDB code: 
protein metals Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
Protein chains
223 a.a. *
50 a.a. *
Waters ×135
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase inhibitor
Title: Complex of bdellastasin with porcine trypsin
Structure: Trypsin. Chain: a. Bdellastasin. Chain: b. Engineered: yes
Source: Sus scrofa. Pig. Organism_taxid: 9823. Secretion: saliva. Hirudo medicinalis. Medicinal leech. Organism_taxid: 6421. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932
Biol. unit: Dimer (from PQS)
2.80Å     R-factor:   0.185     R-free:   0.227
Authors: U.Rester
Key ref:
U.Rester et al. (1999). Structure of the complex of the antistasin-type inhibitor bdellastasin with trypsin and modelling of the bdellastasin-microplasmin system. J Mol Biol, 293, 93. PubMed id: 10512718 DOI: 10.1006/jmbi.1999.3162
03-Aug-99     Release date:   03-Aug-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00761  (TRYP_PIG) -  Trypsin
231 a.a.
223 a.a.*
Protein chain
Pfam   ArchSchema ?
P82107  (BDEL_HIRME) -  Bdellastasin
59 a.a.
50 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chain A: E.C.  - Trypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     digestion   4 terms 
  Biochemical function     catalytic activity     9 terms  


DOI no: 10.1006/jmbi.1999.3162 J Mol Biol 293:93 (1999)
PubMed id: 10512718  
Structure of the complex of the antistasin-type inhibitor bdellastasin with trypsin and modelling of the bdellastasin-microplasmin system.
U.Rester, W.Bode, M.Moser, M.A.Parry, R.Huber, E.Auerswald.
The serine proteinase plasmin is, together with tissue-type plasminogen activator (tPA) and urokinase-type plasminogen activator (uPA), involved in the dissolution of blood clots in a fibrin-dependent manner. Moreover, plasmin plays a key role in a variety of other activation cascades such as the activation of metalloproteinases, and has also been implicated in wound healing, pathogen invasion, cancer invasion and metastasis. The leech-derived (Hirudo medicinalis) antistasin-type inhibitor bdellastasin represents a specific inhibitor of trypsin and plasmin and thus offers a unique opportunity to evaluate the concept of plasmin inhibition. The complexes formed between bdellastasin and bovine as well as porcine beta-trypsin have been crystallised in a monoclinic and a tetragonal crystal form, containing six molecules and one molecule per asymmetric unit, respectively. Both structures have been solved and refined to 3.3 A and 2.8 A resolution. Bdellastasin turns out to have an antistasin-like fold exhibiting a bis-domainal structure like the tissue kallikrein inhibitor hirustasin. The interaction between bdellastasin and trypsin is restricted to the C-terminal subdomain of bdellastasin, particularly to its primary binding loop, comprising residues Asp30-Glu38. The reactive site of bdellastasin differs from other antistasin-type inhibitors of trypsin-like proteinases, exhibiting a lysine residue instead of an arginine residue at P1. A model of the bdellastasin-microplasmin complex has been created based on the X-ray structures. Our modelling studies indicate that both trypsin and microplasmin recognise bdellastasin by interactions which are characteristic for canonically binding proteinase inhibitors. On the basis of our three-dimensional structures, and in comparison with the tissue-kallikrein-bound and free hirustasin and the antistasin structures, we postulate that the binding of the inhibitors toward trypsin and plasmin is accompanied by a switch of the primary binding loop segment P5-P3. Moreover, in the factor Xa inhibitor antistasin, the core of the molecule would prevent an equivalent rotation of the P3 residue, making exosite interactions of antistasin with factor Xa imperative. Furthermore, Arg32 of antistasin would clash with Arg175 of plasmin, thus impairing a favourable antistasin-plasmin interaction and explaining its specificity.
  Selected figure(s)  
Figure 3.
Figure 3. Interaction of the binding loop Asp30 (P5) to Glu38 (P4 ) of bdellastasin with porcine trypsin and micro- plasmin. Stereo view of the interaction between the binding loop of bdellastasin (yellow) with (a) trypsin and with (b) plasmin. The trypsin and the plasmin molecules are represented as stick models superimposed with transparent electrostatic potential surfaces. Positively and negatively charged regions are coloured blue and red, respectively.
Figure 5.
Figure 5. Superposition of antistasin-type inhibitors. (a) Stereo superposition of bdellastasin (blue), tissue-kal- likrein-bound hirustasin (green), and the N-terminal (red) and the C-terminal (magenta) domain of antistasin. The superposition is based on the C a atoms of residues 24-52 of hirustasin and residues 28-55 and 83-110 of the N and C-terminal domains of antistasin, respectively. The N and C-terminal subdomains are indicated. (b) Stereo superposition of the N-terminal subdomains of bdellastasin (blue), tissue-kallikrein-bound hirustasin (green), and subdomains Nn (red) and Cn (magenta) of antistasin. The N and C termini are marked and the residues Glu15 and Glu69 of the interface contact loops of N and C-terminal subdomains of antistasin are high- lighted. Yellow connections indicate disulphide bridges.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 293, 93-0) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
11847284 C.D.Smith, M.Carson, A.M.Friedman, M.M.Skinner, L.Delucas, L.Chantalat, L.Weise, T.Shirasawa, and D.Chattopadhyay (2002).
Crystal structure of human L-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6-A resolution and modeling of an isoaspartyl-containing peptide at the active site.
  Protein Sci, 11, 625-635.
PDB code: 1i1n
10771427 U.Rester, M.Moser, R.Huber, and W.Bode (2000).
L-Isoaspartate 115 of porcine beta-trypsin promotes crystallization of its complex with bdellastasin.
  Acta Crystallogr D Biol Crystallogr, 56, 581-588.
PDB code: 1eja
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.