PDBsum entry 7tln

Go to PDB code: 
protein ligands metals links
Hydrolase (metalloproteinase) PDB id
Protein chain
316 a.a. *
_CA ×4
Waters ×166
* Residue conservation analysis
PDB id:
Name: Hydrolase (metalloproteinase)
Title: Structural analysis of the inhibition of thermolysin by an a site-directed irreversible inhibitor
Structure: Thermolysin. Chain: a. Engineered: yes
Source: Bacillus thermoproteolyticus. Organism_taxid: 1427
2.30Å     R-factor:   0.170    
Authors: B.W.Matthews,M.A.Holmes,D.E.Tronrud
Key ref:
M.A.Holmes et al. (1983). Structural analysis of the inhibition of thermolysin by an active-site-directed irreversible inhibitor. Biochemistry, 22, 236-240. PubMed id: 6830761 DOI: 10.1021/bi00270a034
27-Jan-83     Release date:   09-Mar-83    
Supersedes: 6tln
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)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     metalloendopeptidase activity     1 term  


DOI no: 10.1021/bi00270a034 Biochemistry 22:236-240 (1983)
PubMed id: 6830761  
Structural analysis of the inhibition of thermolysin by an active-site-directed irreversible inhibitor.
M.A.Holmes, D.E.Tronrud, B.W.Matthews.
The mode of binding of the irreversible thermolysin inhibitor ClCH2CO-DL-(N-OH)Leu-OCH3 [Rasnick, D., & Powers, J.C. (1978) Biochemistry 17, 4363-4369] has been determined by X-ray crystallography at a resolution of 2.3 A and the structure of the covalent complex refined to give a crystallographic residual of 17.0%. This is the first such structural study of an active-site-directed covalent complex of a zinc protease. As anticipated by Rasnick and Powers, the inhibitor alkylates Glu-143 in the thermolysin active site, and the hydroxamic acid moiety coordinates the zinc ion. The formation of the covalent complex is associated with a significant shift in a segment of the polypeptide backbone in the vicinity of the active site. This conformational adjustment appears to be necessary to relieve steric hindrance which would otherwise prevent alkylation of Glu-143. It is suggested that this steric hindrance, which occurs for thermolysin but would not be expected for carboxypeptidase A, accounts for the previously inexplicable difference in reactivity of these two metalloproteases toward N-haloacetyl amino acids. The relevance of this steric hindrance to the mechanism of catalysis is discussed. In agreement with previous results [Kester, W. R., & Matthews, B. W. (1977) Biochemistry 16, 2506-2516], it appears that steric hindrance prevents the direct attack of Glu-143 on the carbonyl carbon of an extended substrate, therefore ruling out the anhydride pathway in thermolysin-catalyzed hydrolysis of polypeptide substrates and their ester analogues.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19152630 O.A.Adekoya, and I.Sylte (2009).
The thermolysin family (m4) of enzymes: therapeutic and biotechnological potential.
  Chem Biol Drug Des, 73, 7.  
16640331 S.Zhang, A.Golbraikh, and A.Tropsha (2006).
Development of quantitative structure-binding affinity relationship models based on novel geometrical chemical descriptors of the protein-ligand interfaces.
  J Med Chem, 49, 2713-2724.  
11859085 Kreij, B.van den Burg, G.Venema, G.Vriend, V.G.Eijsink, and J.E.Nielsen (2002).
The effects of modifying the surface charge on the catalytic activity of a thermolysin-like protease.
  J Biol Chem, 277, 15432-15438.  
10201830 D.H.Kim, and Y.Jin (1999).
First hydroxamate inhibitors for carboxypeptidase A. N-acyl-N-hydroxy-beta-phenylalanines.
  Bioorg Med Chem Lett, 9, 691-696.  
9720222 S.Kojima, T.Kumazaki, S.Ishii, and K.Miura (1998).
Primary structure of Streptomyces griseus metalloendopeptidase II.
  Biosci Biotechnol Biochem, 62, 1392-1398.  
7738606 G.Müller, M.Gurrath, and H.Kessler (1994).
Pharmacophore refinement of gpIIb/IIIa antagonists based on comparative studies of antiadhesive cyclic and acyclic RGD peptides.
  J Comput Aided Mol Des, 8, 709-730.  
1576995 H.Nar, R.Huber, A.Messerschmidt, A.C.Filippou, M.Barth, M.Jaquinod, M.van de Kamp, and G.W.Canters (1992).
Characterization and crystal structure of zinc azurin, a by-product of heterologous expression in Escherichia coli of Pseudomonas aeruginosa copper azurin.
  Eur J Biochem, 205, 1123-1129.
PDB code: 1e67
3709536 D.E.Tronrud, A.F.Monzingo, and B.W.Matthews (1986).
Crystallographic structural analysis of phosphoramidates as inhibitors and transition-state analogs of thermolysin.
  Eur J Biochem, 157, 261-268.
PDB codes: 1tlp 2tmn
3514216 J.W.Fox, R.Campbell, L.Beggerly, and J.B.Bjarnason (1986).
Substrate specificities and inhibition of two hemorrhagic zinc proteases Ht-c and Ht-d from Crotalus atrox venom.
  Eur J Biochem, 156, 65-72.  
2988395 D.G.Hangauer, P.Gund, J.D.Andose, B.L.Bush, E.M.Fluder, E.F.McIntyre, and G.M.Smith (1985).
Modeling the mechanism of peptide cleavage by thermolysin.
  Ann N Y Acad Sci, 439, 124-139.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.