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: 34.23 kDa 
• Atom Count: 2638 
• Residue Count: 289 
• Unique protein chains: 2

2PGB

Inhibitor-free human thrombin mutant C191A-C220A

• DOI: 10.2210/pdb2PGB/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2007-04-09 Released: 2007-07-17 
• Deposition Author(s): Bush-Pelc, L.A., Marino, F., Chen, Z., Pineda, A.O., Mathews, F.S., Di Cera, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.217 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 

Literature

Important role of the cys-191 cys-220 disulfide bond in thrombin function and allostery

Bush-Pelc, L.A., Marino, F., Chen, Z., Pineda, A.O., Mathews, F.S., Di Cera, E.

(2007) J Biol Chem 282: 27165-27170

• PubMed: 17636263 
• DOI: 10.1074/jbc.M703202200
• Primary Citation of Related Structures:  
  2PGQ, 2PGB


• PubMed Abstract: 
  

Little is known on the role of disulfide bonds in the catalytic domain of serine proteases. The Cys-191-Cys-220 disulfide bond is located between the 190 strand leading to the oxyanion hole and the 220-loop that contributes to the architecture of the primary specificity pocket and the Na+ binding site in allosteric proteases. Removal of this bond in thrombin produces an approximately 100-fold loss of activity toward several chromogenic and natural substrates carrying Arg or Lys at P1. Na+ activation is compromised, and no fluorescence change can be detected in response to Na+ binding. A 1.54-A resolution structure of the C191A/C220A mutant in the free form reveals a conformation similar to the Na+-free slow form of wild type. The lack of disulfide bond exposes the side chain of Asp-189 to solvent, flips the backbone O atom of Gly-219, and generates disorder in portions of the 186 and 220 loops defining the Na+ site. This conformation, featuring perturbation of the Na+ site but with the active site accessible to substrate, offers a possible representation of the recently identified E* form of thrombin. Disorder in the 186 and 220 loops and the flip of Gly-219 are corrected by the active site inhibitor H-D-Phe-Pro-Arg-CH(2)Cl, as revealed by the 1.8-A resolution structure of the complex. We conclude that the Cys-191-Cys-220 disulfide bond confers stability to the primary specificity pocket by shielding Asp-189 from the solvent and orients the backbone O atom of Gly-219 for optimal substrate binding. In addition, the disulfide bond stabilizes the 186 and 220 loops that are critical for Na+ binding and activation.

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Related Citations: 

• Molecular dissection of Na+ binding to thrombin
  Pineda, A.O., Carrell, C.J., Bush, L.A., Prasad, S., Caccia, S., Chen, Z.W., Mathews, F.S., Di Cera, E.
  (2004) J Biol Chem 279: 31842

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A	36	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): 2  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
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.217 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.412	α = 90
b = 96.597	β = 90
c = 48.14	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-04-09 
• Released Date: 2007-07-17 
Deposition Author(s): Bush-Pelc, L.A., Marino, F., Chen, Z., Pineda, A.O., Mathews, F.S., Di Cera, E.

Revision History 

• Version 1.0: 2007-07-17
  Type: Initial release
  
• Version 1.1: 2008-04-21
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary