PDBsum entry 1l3f

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protein metals links
Hydrolase PDB id
Protein chain
316 a.a. *
_ZN ×3
_CA ×4
Waters ×127
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Thermolysin in the absence of substrate has an open conformation
Structure: Thermolysin. Chain: e. Ec:
Source: Bacillus thermoproteolyticus. Organism_taxid: 1427
2.30Å     R-factor:   0.202     R-free:   0.302
Authors: A.C.Hausrath,B.W.Matthews
Key ref:
A.C.Hausrath and B.W.Matthews (2002). Thermolysin in the absence of substrate has an open conformation. Acta Crystallogr D Biol Crystallogr, 58, 1002-1007. PubMed id: 12037302 DOI: 10.1107/S090744490200584X
26-Feb-02     Release date:   03-Jul-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00800  (THER_BACTH) -  Thermolysin
548 a.a.
316 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Thermolysin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Xaa-|-Leu > Xaa-|-Phe.
      Cofactor: Ca(2+); Zn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     metalloendopeptidase activity     1 term  


DOI no: 10.1107/S090744490200584X Acta Crystallogr D Biol Crystallogr 58:1002-1007 (2002)
PubMed id: 12037302  
Thermolysin in the absence of substrate has an open conformation.
A.C.Hausrath, B.W.Matthews.
The bacterial neutral proteases have been proposed to undergo hinge-bending during their catalytic cycle. However, in thermolysin, the prototypical member of the family, no significant conformational change has been observed. The structure of thermolysin has now been determined in a new crystal form that for the first time shows the enzyme in the absence of a ligand bound in the active site. This is shown to be an 'open' form of the enzyme. The relative orientation of the two domains that define the active-site cleft differ by a 5 degrees rotation relative to their positions in the previously studied ligand-bound 'closed' form. Based on structural comparisons, kinetic studies on mutants and molecular-dynamics simulations, Gly78 and Gly135-Gly136 have previously been suggested as two possible hinge regions. Comparison of the 'open' and 'closed' structures suggests that neither of the proposed hinge regions completely accounts for the observed displacement. The concerted movement of a group of side chains suggested to be associated with the hinge-bending motion is, however, confirmed.
  Selected figure(s)  
Figure 1.
Figure 1 Superposition of the backbone structures of the `closed' (blue) and `open' (red) forms of thermolysin. The structures are superimposed based on the C-terminal domain (residues 78-90, 135-194 and 200-316; Holland et al., 1992[Holland, D. R., Tronrud, D. E., Pley, H. W., Flaherty, K. M., Stark, W., Jansonius, J. N., McKay, D. B. & Matthews, B. W. (1992). Biochemistry, 31, 11310-11316.]).
Figure 4.
Figure 4 (a) Plot showing the distance of each C^ atom in the closed form of thermolysin from the hinge-bending axis. The axis was defined by superimposing the C-terminal domains of the open and closed forms of the enzyme (as in Fig. 1-) and then using EDPDB (Zhang & Matthews, 1995[Zhang, X.-J. & Matthews, B. W. (1995). J. Appl. Cryst. 28, 624-630.]) to determine the axis of rotation that relates the N-terminal domains. In this calculation, the N-terminal domain was taken to include residues 1-77, 92-134 and 195-199, while the C-terminal domain was comprised of residues 78-90, 135-194 and 200-316. (b) Magnitude of the difference in distances from the hinge-bending axis between the open and closed forms of thermolysin.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 1002-1007) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21525640 D.H.Juers, and M.Weik (2011).
Similarities and differences in radiation damage at 100 K versus 160 K in a crystal of thermolysin.
  J Synchrotron Radiat, 18, 329-337.  
19915005 I.V.Demidyuk, T.Y.Gromova, K.M.Polyakov, W.R.Melik-Adamyan, I.P.Kuranova, and S.V.Kostrov (2010).
Crystal structure of the protealysin precursor: insights into propeptide function.
  J Biol Chem, 285, 2003-2013.
PDB code: 2vqx
19458713 E.Erez, D.Fass, and E.Bibi (2009).
How intramembrane proteases bury hydrolytic reactions in the membrane.
  Nature, 459, 371-378.  
19152630 O.A.Adekoya, and I.Sylte (2009).
The thermolysin family (m4) of enzymes: therapeutic and biotechnological potential.
  Chem Biol Drug Des, 73, 7.  
16601675 K.A.Johnson, S.Bhushan, A.Ståhl, B.M.Hallberg, A.Frohn, E.Glaser, and T.Eneqvist (2006).
The closed structure of presequence protease PreP forms a unique 10,000 Angstroms3 chamber for proteolysis.
  EMBO J, 25, 1977-1986.
PDB code: 2fge
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