Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 34.11 kDa 
• Atom Count: 2490 
• Residue Count: 275 
• Unique protein chains: 2

3S7H

Structure of thrombin mutant Y225P in the E* form

• DOI: 10.2210/pdb3S7H/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2011-05-26 Released: 2011-07-06 
• Deposition Author(s): Niu, W., Chen, Z., Gandhi, P., Vogt, A., Pozzi, N., Pele, L.A., Zapata, F., Di Cera, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.204 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

Crystallographic and Kinetic Evidence of Allostery in a Trypsin-like Protease.

Niu, W., Chen, Z., Gandhi, P.S., Vogt, A.D., Pozzi, N., Pelc, L.A., Zapata, F., Di Cera, E.

(2011) Biochemistry 50: 6301-6307

• PubMed: 21707111 
• DOI: 10.1021/bi200878c
• Primary Citation of Related Structures:  
  3QGN, 3S7H, 3S7K


• PubMed Abstract: 
  

Protein allostery is based on the existence of multiple conformations in equilibrium linked to distinct functional properties. Although evidence of allosteric transitions is relatively easy to identify by functional studies, structural detection of a pre-existing equilibrium between alternative conformations remains challenging even for textbook examples of allosteric proteins. Kinetic studies show that the trypsin-like protease thrombin exists in equilibrium between two conformations where the active site is either collapsed (E*) or accessible to substrate (E). However, structural demonstration that the two conformations exist in the same enzyme construct free of ligands has remained elusive. Here we report the crystal structure of the thrombin mutant N143P in the E form, which complements the recently reported structure in the E* form, and both the E and E* forms of the thrombin mutant Y225P. The side chain of W215 moves 10.9 Å between the two forms, causing a displacement of 6.6 Å of the entire 215-217 segment into the active site that in turn opens or closes access to the primary specificity pocket. Rapid kinetic measurements of p-aminobenzamidine binding to the active site confirm the existence of the E*-E equilibrium in solution for wild-type and the mutants N143P and Y225P. These findings provide unequivocal proof of the allosteric nature of thrombin and lend strong support to the recent proposal that the E*-E equilibrium is a key property of the trypsin fold.

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Related Citations: 

• Structural identification of the pathway of long-range communication in an allosteric enzyme.
  Gandhi, P.S., Chen, Z., Mathews, F.S., Di Cera, E.
  (2008) Proc Natl Acad Sci U S A 105: 1832

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Organizational Affiliation: 

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	35	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.204 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.62	α = 90
b = 57.62	β = 90
c = 119.914	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: 2011-05-26 
• Released Date: 2011-07-06 
Deposition Author(s): Niu, W., Chen, Z., Gandhi, P., Vogt, A., Pozzi, N., Pele, L.A., Zapata, F., Di Cera, E.

Revision History 

• Version 1.0: 2011-07-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-24
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary