1HT3 | pdb_00001ht3

MERCURY INDUCED MODIFICATIONS IN THE STEREOCHEMISTRY OF THE ACTIVE SITE THROUGH CYS-73 IN A SERINE PROTEASE: CRYSTAL STRUCTURE OF THE COMPLEX OF A PARTIALLY MODIFIED PROTEINASE K WITH MERCURY AT 1.8 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.221 (Depositor) 
  • R-Value Work: 
    0.164 (Depositor) 
  • R-Value Observed: 
    0.164 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Mercury induced modifications in the stereochemistry of the active site through Cys-73 in a serine protease--crystal structure of the complex of a partially modified proteinase K with mercury at 1.8 A resolution

Gourinath, S.Degenhardt, M.Eschenburg, S.Moore, K.Delucas, L.J.Betzel, C.H.Singh, T.P.

(2001) Indian J Biochem Biophys 38: 298-302

  • Primary Citation Related Structures: 
    1HT3

  • PubMed Abstract: 

    Proteinese K (PK) isolated from Tritirachium album Limber was crystallized with HgCl2 in excess, under microgravity conditions. The intensity data were collected at 4 degrees C to 1.8 A resolution and the final R-factor after refinement for all the reflections was 0.164. Mercury has been found at two sites with partial occupancies (0.4 and 0.6) which are at distances of 2.48 A and 2.58 A respectively from Cys-73 Sgamma. The Cys-73 in the enzyme structure is located close to the active site residue, His-69. This region is completely buried and is not accessible to the solvent. It is rather tightly packed. Therefore, the binding of mercury distorts the stereochemistry of the neighbouring residues including those belonging to the catalytic triad. As a result of this, the Ogamma of Ser-224 is displaced by 0.6 A which causes the inactivation of proteinase K by increasing the H-bond distance to 3.7 A between Ser-224 Ogamma and His-69 Nepsilon2.


  • Organizational Affiliation
    • Department of Biophysics, All India Institute of Medical Sciences, New Delhi.

Macromolecule Content 

  • Total Structure Weight: 29.4 kDa 
  • Atom Count: 2,278 
  • Modeled Residue Count: 279 
  • Deposited Residue Count: 279 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEINASE K279Parengyodontium albumMutation(s): 0 
EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06873
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.221 (Depositor) 
  • R-Value Work:  0.164 (Depositor) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.36α = 90
b = 68.36β = 90
c = 108.7γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Database references
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary