4HFP

Structure of thrombin mutant S195a bound to the active site inhibitor argatroban

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Autoactivation of thrombin precursors.

Pozzi, N., Chen, Z., Zapata, F., Niu, W., Barranco-Medina, S., Pelc, L.A., Di Cera, E.

(2013) J.Biol.Chem. 288: 11601-11610

  • DOI: 10.1074/jbc.M113.451542
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Trypsin-like proteases are synthesized as inactive zymogens and convert to the mature form upon activation by specific enzymes, often assisted by cofactors. Central to this paradigm is that the zymogen does not convert spontaneously to the mature enz ...

    Trypsin-like proteases are synthesized as inactive zymogens and convert to the mature form upon activation by specific enzymes, often assisted by cofactors. Central to this paradigm is that the zymogen does not convert spontaneously to the mature enzyme, which in turn does not feed back to activate its zymogen form. In the blood, the zymogens prothrombin and prethrombin-2 require the prothrombinase complex to be converted to the mature protease thrombin, which is unable to activate prothrombin or prethrombin-2. Here, we show that replacement of key residues within the activation domain causes these zymogens to spontaneously convert to thrombin. The conversion is started by the zymogen itself, which is capable of binding ligands at the active site, and is abrogated by inactivation of the catalytic residue Ser-195. The product of autoactivation is functionally and structurally equivalent to wild-type thrombin. Zymogen autoactivation is explained by conformational selection, a basic property of the trypsin fold uncovered by structural and rapid kinetics studies. Both the zymogen and protease undergo a pre-existing equilibrium between active and inactive forms. The equilibrium regulates catalytic activity in the protease and has the potential to unleash activity in the zymogen to produce autoactivation. A new strategy emerges for the facile production of enzymes through zymogen autoactivation that is broadly applicable to trypsin-like proteases of biotechnological and clinical interest.

    Organizational Affiliation: 

    Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
A, C
31Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
B, D
259Homo sapiensMutation(s): 1 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
B, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
15U
Query on 15U
Download SDF File 
Download CCD File 
B, D
(2R,4R)-4-methyl-1-(N~2~-{[(3S)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}-L-arginyl)piperidine-2-carboxylic acid
S-argatroban
C23 H36 N6 O5 S
KXNPVXPOPUZYGB-MXSMSXNCSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000889 (15U)
Query on PRD_000889		BS-argatrobanPeptide-like / Inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
15UKd: 42 nM BINDINGMOAD
15UKd: 42 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.167 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 77.229α = 90.00
b = 77.229β = 90.00
c = 94.875γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data scaling
HKL-2000data reduction
CrystalCleardata collection
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-13
    Type: Initial release
  • Version 1.1: 2013-04-10
    Type: Other
  • Version 1.2: 2013-05-22
    Type: Database references