1Z0W

Crystal Structure of A. fulgidus Lon proteolytic domain at 1.2A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Atomic-resolution Crystal Structure of the Proteolytic Domain of Archaeoglobus fulgidus Lon Reveals the Conformational Variability in the Active Sites of Lon Proteases

Botos, I.Melnikov, E.E.Cherry, S.Kozlov, S.Makhovskaya, O.V.Tropea, J.E.Gustchina, A.Rotanova, T.V.Wlodawer, A.

(2005) J Mol Biol 351: 144-157

  • DOI: 10.1016/j.jmb.2005.06.008
  • Primary Citation of Related Structures:  
    1Z0E, 1Z0C, 1Z0B, 1Z0W, 1Z0G

  • PubMed Abstract: 
  • The atomic-resolution crystal structure of the proteolytic domain (P-domain, residues 415-621) of Archaeoglobus fulgidus B-type Lon protease (wtAfLonB) and the structures of several mutants have revealed significant differences in the conformation of ...

    The atomic-resolution crystal structure of the proteolytic domain (P-domain, residues 415-621) of Archaeoglobus fulgidus B-type Lon protease (wtAfLonB) and the structures of several mutants have revealed significant differences in the conformation of the active-site residues when compared to other known Lon P-domains, despite the conservation of the overall fold. The catalytic Ser509 is facing the solvent and is distant from Lys552, the other member of the catalytic dyad. Instead, the adjacent Asp508 forms an ion pair with the catalytic lysine residue. Glu506, an analog of the putative third catalytic residue from a related Methanococcus jannaschii LonB, also faces the solvent and does not interact with the catalytic dyad. We have established that full-length wtAfLonB is proteolytically active in an ATP-dependent manner. The loss of enzymatic activity of the S509A mutant confirms the functional significance of this residue, while retention of considerable level of activity by the D508A and E506A mutants rules out their critical involvement in catalysis. In contrast to the full-length enzymes, all individually purified P-domains (wild-type and mutants) were inactive, and the mutations had no influence on the active-site structure. These findings raise the possibility that, although isolated proteolytic domains of both AfLonB and E.coli LonA are able to assemble into expected functional hexamers, the presence of the other domains, as well as substrate binding, may be needed to stabilize the productive conformation of their active sites. Thus, the observed conformational variability may reflect the differences in the stability of active-site structures for the proteolytic counterparts of single-chain Lon versus independently folded proteolytic subunits of two-chain AAA+ proteases.


    Related Citations: 
    • Pathological crystallography: case studies of several unusual macromolecular crystals
      Dauter, Z., Botos, I., LaRonde-LeBlanc, N., Wlodawer, A.
      (2005) Acta Crystallogr D Biol Crystallogr 61: 967

    Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative protease La homolog typeA207Archaeoglobus fulgidusMutation(s): 0 
EC: 3.4.21.53 (PDB Primary Data), 3.4.21 (UniProt)
Find proteins for O29883 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Explore O29883 
Go to UniProtKB:  O29883
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.137 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.47α = 90
b = 84.47β = 90
c = 41.5γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SHELXL-97refinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance