1SSX

0.83A resolution crystal structure of alpha-lytic protease at pH 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.83 Å
  • R-Value Free: 0.099 
  • R-Value Work: 0.086 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 0.83A Resolution Crystal Structure of alpha-Lytic Protease Reveals the Detailed Structure of the Active Site and Identifies a Source of Conformational Strain.

Fuhrmann, C.N.Kelch, B.A.Ota, N.Agard, D.A.

(2004) J.Mol.Biol. 338: 999-1013

  • DOI: 10.1016/j.jmb.2004.03.018
  • Also Cited By: 3M7U, 3M7T

  • PubMed Abstract: 
  • The crystal structure of the extracellular bacterial serine protease alpha-lytic protease (alphaLP) has been solved at 0.83 A resolution at pH 8. This ultra-high resolution structure allows accurate analysis of structural elements not possible with p ...

    The crystal structure of the extracellular bacterial serine protease alpha-lytic protease (alphaLP) has been solved at 0.83 A resolution at pH 8. This ultra-high resolution structure allows accurate analysis of structural elements not possible with previous structures. Hydrogen atoms are visible, and confirm active-site hydrogen-bonding interactions expected for the apo enzyme. In particular, His57 N(delta1) participates in a normal hydrogen bond with Asp102 in the catalytic triad, with a hydrogen atom visible 0.83(+/-0.06)A from the His N(delta1). The catalytic Ser195 occupies two conformations, one corresponding to a population of His57 that is doubly protonated, the other to the singly protonated His57. Based on the occupancy of these conformations, the pKa of His57 is calculated to be approximately 8.8 when a sulfate ion occupies the active site. This 0.83 A structure has allowed critical analysis of geometric distortions within the structure. Interestingly, Phe228 is significantly distorted from planarity. The distortion of Phe228, buried in the core of the C-terminal domain, occurs at an estimated energetic cost of 4.1 kcal/mol. The conformational space for Phe228 is severely limited by the presence of Trp199, which prevents Phe228 from adopting the rotamer observed in many other chymotrypsin family members. In alphaLP, the only allowed rotamer leads to the deformation of Phe228 due to steric interactions with Thr181. We hypothesize that tight packing of co-evolved residues in this region, and the subsequent deformation of Phe228, contributes to the high cooperativity and large energetic barriers for folding and unfolding of alphaLP. The kinetic stability imparted by the large, cooperative unfolding barrier plays a critical role in extending the lifetime of the protease in its harsh environment.


    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-lytic protease
A
198Lysobacter enzymogenesMutation(s): 0 
Gene Names: alpha-LP
EC: 3.4.21.12
Find proteins for P00778 (Lysobacter enzymogenes)
Go to UniProtKB:  P00778
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.83 Å
  • R-Value Free: 0.099 
  • R-Value Work: 0.086 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 65.910α = 90.00
b = 65.910β = 90.00
c = 79.697γ = 120.00
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALEPACKdata scaling
SHELXmodel building
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance