1QY6 | pdb_00001qy6

Structue of V8 Protease from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.230 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1QY6

This is version 1.3 of the entry. See complete history

Literature

The structure of a universally employed enzyme: V8 protease from Staphylococcus aureus.

Prasad, L.Leduc, Y.Hayakawa, K.Delbaere, L.T.

(2004) Acta Crystallogr D Biol Crystallogr 60: 256-259

  • DOI: https://doi.org/10.1107/S090744490302599X
  • Primary Citation Related Structures: 
    1QY6, 2O8L

  • PubMed Abstract: 

    V8 protease, an extracellular protease of Staphylococcus aureus, is related to the pancreatic serine proteases. The enzyme cleaves peptide bonds exclusively on the carbonyl side of aspartate and glutamate residues. Unlike the pancreatic serine proteases, V8 protease possesses no disulfide bridges. This is a major evolutionary difference, as all pancreatic proteases have at least two disulfide bridges. The structure of V8 protease shows structural similarity with several other serine proteases, specifically the epidermolytic toxins A and B from S. aureus and trypsin, in which the conformation of the active site is almost identical. V8 protease is also unique in that the positively charged N-terminus is involved in determining the substrate-specificity of the enzyme.


  • Organizational Affiliation
    • Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.

Macromolecule Content 

  • Total Structure Weight: 29.71 kDa 
  • Atom Count: 1,715 
  • Modeled Residue Count: 216 
  • Deposited Residue Count: 274 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
serine protease274Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
EC: 3.4.21.19
UniProt
Find proteins for Q99V45 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore Q99V45 
Go to UniProtKB:  Q99V45
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99V45
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K

Query on K



Download:Ideal Coordinates CCD File
B [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.230 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.721α = 90
b = 62.721β = 90
c = 225.876γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
X-PLORrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations