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PDBsum entry 3flf

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protein ligands metals links
Hydrolase PDB id
3flf
Jmol
Contents
Protein chain
316 a.a. *
Ligands
UB3
GOL ×2
Metals
_CA ×4
_ZN
Waters ×219
* Residue conservation analysis
PDB id:
3flf
Name: Hydrolase
Title: Thermolysin inhibition
Structure: Thermolysin. Chain: a. Fragment: unp residues 233-548. Synonym: thermostable neutral proteinase. Ec: 3.4.24.27
Source: Bacillus thermoproteolyticus. Organism_taxid: 1427
Resolution:
1.97Å     R-factor:   0.202     R-free:   0.265
Authors: L.Englert,Biela A.,A.Heine,G.Klebe
Key ref: L.Englert et al. (2010). Displacement of disordered water molecules from hydrophobic pocket creates enthalpic signature: binding of phosphonamidate to the S₁'-pocket of thermolysin. Biochim Biophys Acta, 1800, 1192-1202. PubMed id: 20600625 DOI: 10.1016/j.bbagen.2010.06.009
Date:
18-Dec-08     Release date:   12-Jan-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00800  (THER_BACTH) -  Thermolysin
Seq:
Struc:
 
Seq:
Struc:
548 a.a.
316 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.24.27  - Thermolysin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Xaa-|-Leu > Xaa-|-Phe.
      Cofactor: Calcium; Zinc
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     metalloendopeptidase activity     1 term  

 

 
DOI no: 10.1016/j.bbagen.2010.06.009 Biochim Biophys Acta 1800:1192-1202 (2010)
PubMed id: 20600625  
 
 
Displacement of disordered water molecules from hydrophobic pocket creates enthalpic signature: binding of phosphonamidate to the S₁'-pocket of thermolysin.
L.Englert, A.Biela, M.Zayed, A.Heine, D.Hangauer, G.Klebe.
 
  ABSTRACT  
 
BACKGROUND: Prerequisite for the design of tight binding protein inhibitors and prediction of their properties is an in-depth understanding of the structural and thermodynamic details of the binding process. A series of closely related phosphonamidates was studied to elucidate the forces underlying their binding affinity to thermolysin. The investigated inhibitors are identical except for the parts penetrating into the hydrophobic S(1)'-pocket. METHODS: A correlation of structural, kinetic and thermodynamic data was carried out by X-ray crystallography, kinetic inhibition assay and isothermal titration calorimetry. RESULTS & CONCLUSIONS: Binding affinity increases with larger ligand hydrophobic P(1)'-moieties accommodating the S(1)'-pocket. Surprisingly, larger P(1)'-side chain modifications are accompanied by an increase in the enthalpic contribution to binding. In agreement with other studies, it is suggested that the release of largely disorder waters from an imperfectly hydrated pocket results in an enthalpically favourable integration of these water molecules into bulk water upon inhibitor binding. This enthalpically favourable process contributes more strongly to the binding energetics than the entropy increase resulting from the release of water molecules from the S(1)'-pocket or the formation of apolar interactions between protein and inhibitor. GENERAL SIGNIFICANCE: Displacement of highly disordered water molecules from a rather imperfectly hydrated and hydrophobic specificity pocket can reveal an enthalpic signature of inhibitor binding.