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PDBsum entry 1tli

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protein ligands metals links
Hydrolase PDB id
1tli
Jmol
Contents
Protein chain
316 a.a. *
Ligands
DMS
Metals
_ZN
_CA ×4
Waters ×149
* Residue conservation analysis
PDB id:
1tli
Name: Hydrolase
Title: Thermolysin (2% isopropanol soaked crystals)
Structure: Thermolysin. Chain: a. Ec: 3.4.24.27
Source: Bacillus thermoproteolyticus. Organism_taxid: 1427
Biol. unit: Dimer (from PQS)
Resolution:
2.05Å     R-factor:   0.165     R-free:   0.219
Authors: A.C.English,S.H.Done,C.R.Groom,R.E.Hubbard
Key ref:
A.C.English et al. (1999). Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol. Proteins, 37, 628-640. PubMed id: 10651278 DOI: 10.1002/(SICI)1097-0134(19991201)37:4<628::AID-PROT13>3.3.CO;2-7
Date:
27-Oct-98     Release date:   18-Feb-00    
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
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.4.24.27  - 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: 10.1002/(SICI)1097-0134(19991201)37:4<628::AID-PROT13>3.3.CO;2-7 Proteins 37:628-640 (1999)
PubMed id: 10651278  
 
 
Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol.
A.C.English, S.H.Done, L.S.Caves, C.R.Groom, R.E.Hubbard.
 
  ABSTRACT  
 
Multiple-solvent crystal structure determination (MSCS) allows the position and orientation of bound solvent fragments to be identified by determining the structure of protein crystals soaked in organic solvents. We have extended this technique by the determination of high-resolution crystal structures of thermolysin (TLN), generated from crystals soaked in 2% to 100% isopropanol. The procedure causes only minor changes to the conformation of the protein, and an increasing number of isopropanol interaction sites could be identified as the solvent concentration is increased. Isopropanol occupies all four of the main subsites in the active site, although this was only observed at very high concentrations of isopropanol for three of the four subsites. Analysis of the isopropanol positions shows little correlation with interaction energy computed using a molecular mechanics force field, but the experimentally determined positions of isopropanol are consistent with the structures of known protein-ligand complexes of TLN.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo drawings to show isopropanol binding reducing the disorder in the interior of TLN. A shows the refined TLN-0 structure. B and C show the refined TLN-10 structure. Red cpk spheres denote bound water molecules in A, B and C. A. 2mF[o(nat)]-DF[c] map (contoured at 1.2 ), at a resolution of 1.65 Å. The side chains of M120 and E143 are disordered. B. 2mF[o(ipa,10)]-DF[c] map (contoured at 1.2 ), at a resolution of 1.95 Å. The side chains of M120 and E143 are in a single conformer, and L144 has changed conformation, highlighting a concerted re-packing .[11] C. mF[o(ipa,10)]-mF[o(nat)] difference density map (contoured at ±5.0 ) (1.95 Å). Positive and negative difference density are shown in green and red, respectively. For clarity, the alternate B conformers of the M120 and E143 side chains, and the original conformation of L144 in the TLN-0 structure have been superimposed (colored yellow). The phases were calculated from the refined TLN-0 model (see Materials and Methods).
Figure 3.
Figure 3. Stereo drawing showing isopropanol (IPA 6) binding at a crystal contact in TLN. The figure shows the mF[o(ipa,90)] map (contoured at 0.3 ), at a resolution of 1.95 Å superimposed with the refined TLN-90 model. Red cpk spheres denote bound water molecules, and yellow bonds indicate the symmetry-related molecule. A nearby molecule of water (B value 28.5 Å^2) was also omitted from the model when calculating the map, to highlight the differences in shape between the electron density of isopropanol and water. For clarity, the mF[o(ipa,90)] map is displayed only over IPA 6 and a nearby water molecule.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (1999, 37, 628-640) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23275160 A.Ruf, M.Stihle, J.Benz, M.Schmidt, and H.Sobek (2013).
Structure of Gentlyase, the neutral metalloprotease of Paenibacillus polymyxa.
  Acta Crystallogr D Biol Crystallogr, 69, 24-31.
PDB codes: 4b52 4ger
22194332 M.Mueller, M.Wang, and C.Schulze-Briese (2012).
Optimal fine φ-slicing for single-photon-counting pixel detectors.
  Acta Crystallogr D Biol Crystallogr, 68, 42-56.  
20459833 D.H.Bryant, M.Moll, B.Y.Chen, V.Y.Fofanov, and L.E.Kavraki (2010).
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction.
  BMC Bioinformatics, 11, 242.  
19176554 R.Brenke, D.Kozakov, G.Y.Chuang, D.Beglov, D.Hall, M.R.Landon, C.Mattos, and S.Vajda (2009).
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques.
  Bioinformatics, 25, 621-627.  
17163509 J.Mansfeld, and R.Ulbrich-Hofmann (2007).
The stability of engineered thermostable neutral proteases from Bacillus stearothermophilus in organic solvents and detergents.
  Biotechnol Bioeng, 97, 672-679.  
18063795 L.Feng, H.Yan, Z.Wu, N.Yan, Z.Wang, P.D.Jeffrey, and Y.Shi (2007).
Structure of a site-2 protease family intramembrane metalloprotease.
  Science, 318, 1608-1612.
PDB code: 3b4r
17139084 W.C.Ho, C.Luo, K.Zhao, X.Chai, M.X.Fitzgerald, and R.Marmorstein (2006).
High-resolution structure of the p53 core domain: implications for binding small-molecule stabilizing compounds.
  Acta Crystallogr D Biol Crystallogr, 62, 1484-1493.
PDB codes: 2ioi 2iom 2ioo
15908573 D.Kozakov, K.H.Clodfelter, S.Vajda, and C.J.Camacho (2005).
Optimal clustering for detecting near-native conformations in protein docking.
  Biophys J, 89, 867-875.  
15608178 S.H.Sheu, D.R.Lancia, K.H.Clodfelter, M.R.Landon, and S.Vajda (2005).
PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes.
  Nucleic Acids Res, 33, D206-D211.  
12557186 S.C.Lovell, I.W.Davis, W.B.Arendall, P.I.de Bakker, J.M.Word, M.G.Prisant, J.S.Richardson, and D.C.Richardson (2003).
Structure validation by Calpha geometry: phi,psi and Cbeta deviation.
  Proteins, 50, 437-450.  
11679714 K.Harata, W.D.Schubert, and M.Muraki (2001).
Structure of Urtica dioica agglutinin isolectin I: dimer formation mediated by two zinc ions bound at the sugar-binding site.
  Acta Crystallogr D Biol Crystallogr, 57, 1513-1517.
PDB code: 1iqb
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 codes are shown on the right.