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

Experimental Data Snapshot

  • Resolution: 0.83 Å
  • R-Value Free: 0.099 
  • R-Value Work: 0.086 
  • R-Value Observed: 0.087 

Starting Model: experimental
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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: https://doi.org/10.1016/j.jmb.2004.03.018
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-lytic protease198Lysobacter enzymogenesMutation(s): 0 
Gene Names: ALPHA-LP
Find proteins for P00778 (Lysobacter enzymogenes)
Explore P00778 
Go to UniProtKB:  P00778
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00778
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 0.83 Å
  • R-Value Free: 0.099 
  • R-Value Work: 0.086 
  • R-Value Observed: 0.087 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.91α = 90
b = 65.91β = 90
c = 79.697γ = 120
Software Package:
Software NamePurpose
SHELXmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description