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

 

 

 

 

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Contents
Protein chains
36 a.a. *
253 a.a. *
Ligands
ASP-PHE-GLU-GLU-
ILE-PRO-GLU-GLU-
TYS-LEU
NAG
IN2 ×2
Waters ×180
* Residue conservation analysis
PDB id:
1uma
Name: Hydrolase/hydrolase inhibitor
Title: Alpha-thrombin (hirugen) complexed with na-(n,n-dimethylcarbamoyl)- alpha-azalysine
Structure: Alpha-thrombin. Chain: l. Alpha-thrombin. Chain: h. Hirudin i. Chain: i
Source: Homo sapiens. Human. Organism_taxid: 9606. Tissue: plasma. Hirudo medicinalis. Medicinal leech. Organism_taxid: 6421. Tissue: plasma
Biol. unit: Not given
Resolution:
2.00Å     R-factor:   0.168    
Authors: M.Nardini,A.Pesce,M.Rizzi,E.Casale,R.Ferraccioli,G.Balliano,P.Milla, P.Ascenzi,M.Bolognesi
Key ref:
M.Nardini et al. (1996). Human alpha-thrombin inhibition by the active site titrant N alpha-(N,N-dimethylcarbamoyl)-alpha-azalysine p-nitrophenyl ester: a comparative kinetic and X-ray crystallographic study. J Mol Biol, 258, 851-859. PubMed id: 8637015 DOI: 10.1006/jmbi.1996.0292
Date:
26-Mar-96     Release date:   08-Nov-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		622 a.a.
36 a.a.
Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		622 a.a.
253 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.

 

 
DOI no: 10.1006/jmbi.1996.0292 J Mol Biol 258:851-859 (1996)
PubMed id: 8637015  
 
 
Human alpha-thrombin inhibition by the active site titrant N alpha-(N,N-dimethylcarbamoyl)-alpha-azalysine p-nitrophenyl ester: a comparative kinetic and X-ray crystallographic study.
M.Nardini, A.Pesce, M.Rizzi, E.Casale, R.Ferraccioli, G.Balliano, P.Milla, P.Ascenzi, M.Bolognesi.
 
  ABSTRACT  
 
Kinetics for the hydrolysis of the chromogenic active site titrant N alpha-(N,N-dimethylcarbamoyl)-alpha-azalysine p-nitrophenyl ester (Dmc-azaLys-ONp) catalyzed by bovine beta-trypsin, bovine alpha-thrombin, human alpha-thrombin, human Lys77-plasmin, human urinary kallikrein, the M(r) 33,000 and M(r) 54,000 species of human urokinase, as well as by porcine pancreatic beta-kallikrein-A and B have been obtained between pH 6.0 and 8.0, at 21.0 degrees C. Moreover, the three dimensional structure of the human alpha-thrombin-(hirugen).Dmc-azaLys acyl.enzyme complex has been analyzed and refined by X-ray crystallography at 2.0 A resolution (R-factor = 0.168). As observed for bovine beta-trypsin, the acylating inhibitor molecule is covalently bound to the Ser195 catalytic residue, filling the human alpha-thrombin S1 primary specificity subsite with its lysyl side-group. However, the carbonyl group of the scissile human alpha-thrombin.Dmc-azaLys acyl bond does not occupy properly the oxyanion binding hole. At variance from the bovine beta-trypsin.Dmc-azaLys acyl.enzyme structure, a second, not covalently bound, inhibitor molecule, partly shielded by the 60-insertion loop of human alpha-thrombin, is contacting the enzyme "aryl-binding site".
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Chemical structure of Dmc-azaLys-ONp. The O-8 and O-12 atoms of the active site titrant, relevant for the discussion, have been labeled. 		Figure 2.
Figure 2. A, Time-course of p-nitrophenol release during the human a-thrombin (trace a) and bovine a-thrombin (trace b) catalyzed hydrolysis of Dmc-azaLys-ONp at pH 6.2 and 21.0°C, with [S0]e5[E0 ]. Kinetics of p-nitrophenol release were obtained at [Dmc-azaLys-ONp] = 5.0 × 10 2 mM; [E0] was 5.0 mM. The total amplitude of the time-course of p-nitrophenol release (p; see equation (2)) corresponds to an absorbance change of 2.6 × 10 -2 (i.e. to an active enzyme concentration of 5.0 mM). Values of the apparent first-order rate constant of the time-course of p-nitrophenol release (k; s -1 ) are 5.45 s -1 (trace a) and 3.65 s -1 (trace b). B, Effect of the Dmc-azaLys-ONp concentration on the apparent first-order rate constant (k) for the human a-thrombin (open circles) and bovine a-thrombin (filled circles) catalyzed hydrolysis of the active site titrant at pH 6.2 and 21.0°C, with [S0 ]e5 [E0 ]. The continuous lines, representing the best theoretical curves fitting the data, were calculated according to equation (3) with values of KS and k+2 given in Table 1. An average S.E. of 27% was evaluated as the standard deviation for values of KS and k+2 . The arrows indicate the asymptotic values of k that correspond to k+2 when [S0 ]>KS (see equation (3)). For further details, see the text.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 258, 851-859) copyright 1996.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17685615 C.C.Liu, E.Brustad, W.Liu, and P.G.Schultz (2007).
Crystal structure of a biosynthetic sulfo-hirudin complexed to thrombin.
  J Am Chem Soc, 129, 10648-10649.
PDB code: 2pw8
11857638 B.J.McFarland, and C.Beeson (2002).
Binding interactions between peptides and proteins of the class II major histocompatibility complex.
  Med Res Rev, 22, 168-203.  
10672036 P.Ascenzi, G.Balliano, C.Gallina, F.Polticelli, and M.Bolognesi (2000).
Serine proteinase inhibition by the active site titrant N alpha-(N, N-dimethylcarbamoyl)-alpha-azaornithine p-nitrophenyl ester. A comparative study.
  Eur J Biochem, 267, 1239-1246.  
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.  
  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
9811486 R.Cortesi, P.Ascenzi, M.Colasanti, T.Persichini, G.Venturini, M.Bolognesi, A.Pesce, C.Nastruzzi, and E.Menegatti (1998).
Cross-enzyme inhibition by gabexate mesylate: formulation and reactivity study.
  J Pharm Sci, 87, 1335-1340.  
  9792427 S.Tada, and J.J.Blow (1998).
The replication licensing system.
  Biol Chem, 379, 941-949.  
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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