Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 67.89 kDa 
• Atom Count: 4775 
• Modelled Residue Count: 573 
• Deposited Residue Count: 580 
• Unique protein chains: 2

4HFP

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

• PDB DOI: 10.2210/pdb4HFP/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-10-05 Released: 2013-03-13 
• Deposition Author(s): Pozzi, N., Chen, Z., Zapata, F., Lin, W., Barranco-Medina, S., Pelc, L.A., Di Cera, E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.238 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 

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

• PubMed: 23467412 
• DOI: 10.1074/jbc.M113.451542
• Primary Citation of Related Structures:  
  4H6S, 4H6T, 4HFP, 4RN6


• 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 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A, C	31	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	B, D	259	Homo sapiens	Mutation(s): 1  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
15U	F [auth B], H [auth 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 C23 H36 N6 O5 S KXNPVXPOPUZYGB-MXSMSXNCSA-N
NA	E [auth B], G [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
15U	BindingDB:  4HFP	Ki: 20 (nM) from 1 assay(s)
	PDBBind:  4HFP	Kd: 42 (nM) from 1 assay(s)
	Binding MOAD:  4HFP	Kd: 42 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000889 (15U)	F [auth B], H [auth D]	S-argatroban	Peptide-like / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.238 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.229	α = 90
b = 77.229	β = 90
c = 94.875	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-05 
• Released Date: 2013-03-13 
Deposition Author(s): Pozzi, N., Chen, Z., Zapata, F., Lin, W., Barranco-Medina, S., Pelc, L.A., Di Cera, E.

Revision History  

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