::Protein Data Bank (PDB)::

Protein Data Bank 

 

   Protein Data Bank is a repository for 3-D biological macromolecular structure.All data are available to the public.It includes proteins, nucleic acids and viruses.Obtained by X-Ray crystallography (80%) or NMR spectroscopy (16%).Submitted by biologists and biochemists from around the world.Founded in 1971 by Brookhaven National Laboratory, New York.First set of data were entered on punched cards.  Then with magnetic tapes.Transferred to the Research Collaborators for Structural Bioinformatics (RCSB) in 1998.Currently it holds 29,000 released structures.PDB is an important resource for research in the academic,pharmaceutical,and biotechnology sectors.

Those are some example of the sturcture that had been build by using the PDB.

  

Subtilisin

Subtilisin

 

 

  Subtilisin (serine endopeptidase) is a non-specific protease (a protein-digesting enzyme) initially obtained from Bacillus subtilis.

  Subtilisins belong to subtilases, a group of serine proteases that initiate the nucleophilicpeptide (amide) bond through a serine residue at the active site. They are physically and chemically well-characterized enzymes. Subtilisins typically have molecular weights of about 20,000 to 45,000 dalton. They can be obtained from soil bacteria, for example, Bacillus amyloliquefaciens. Subtilisins are secreted in large amounts from many Bacillus species. attack on the

  Subtilisins are widely used in commercial products, for example, in laundry and dishwashing detergents, cosmetics, food processing , skin care ointments, contact lens cleaners, and for research purposes in synthetic organic chemistry.

  The structure of subtilisin has been determined by X-ray crystallography. It is a 275-residue globular protein with several alpha-helices, and a large beta-sheet. It is structurally unrelated to the chymotrypsin-clan of serine proteases, but uses the same type of catalytic triad in the active site. This makes it the classic example of convergent evolution.

In molecular biology using B. subtilis as a model organism, the gene encoding subtilisin (aprE) is often the second gene of choice after amyE for integrating reporter constructs into, due to its dispensability.

  The active site features a charge-relay network involving Asp-32, His-64, and active site Ser-221 arranged in a catalytic triad. The charge-relay network functions as follows: The carboxylate side-chain of Asp-32 hydrogen-bonds to a nitrogen-bonded proton on His-64's imidazole ring. This is possible because Asp is negatively charged at physiological pH. The other nitrogen on His-64 hydrogen-bonds to the O-H proton of Ser-221. This last interaction results in charge-separation of O-H, with the oxygen atom being more nucleophilic. This allows the oxygen atom of Ser-221 to attack incoming substrates (i.e., peptide bonds), assisted by a neighboring carboxyamide side-chain of Asn-155.

  Even though Asp-32, His-64, and Ser-221 are sequentially far apart, they converge in the 3D structure to form the active site.

  To summarize the interactions described above, Ser-221 acts as a nucleophile and cleaves peptide bonds with its partially negative oxygen atom. This is possible due to the nature of the charge-relay site of subtilisin.

Prolyl aminopeptidase

Prolyl aminopeptidase

The prolyl aminopeptidase complexes of Ala-TBODA [2-alanyl-5-tert-butyl-(1, 3,4)-oxadiazole] and Sar-TBODA [2-sarcosyl-5-tert-butyl-(1, 3, 4)-oxadiazole] were analyzed by X-ray crystallography at 2.4 angstroms resolution. Frames of alanine and sarcosine residues were well superimposed on each other in the pyrrolidine ring of proline residue, suggesting that Ala and Sar are recognized as parts of this ring of proline residue by the presence of a hydrophobic proline pocket at the active site. Interestingly, there was an unusual extraspace at the bottom of the hydrophobic pocket where proline residue is fixed in the prolyl aminopeptidase. Moreover, 4-acetyloxyproline-betaNA (4-acetyloxyproline beta-naphthylamide)better substrate than Pro-betaNA. Computer docking simulation well supports the idea that the 4-acetyloxyl group of the substrate fitted into that space. Alanine scanning mutagenesis of Phe139, Tyr149, Tyr150, Phe236, and Cys271, consisting of the hydrophobic pocket, revealed that all of these five residues are involved significantly in the formation of the hydrophobic proline pocket for the substrate. Tyr149 and Cys271 may be important for the extra space and may orient the acetyl derivative of hydroxyproline to a preferable position for hydrolysis. These findings imply that the efficient degradation of collagen fragment may be achieved through an was a acetylation process by the bacteria.

Lex A repressor

Lex A repressor

Repressor LexA or LexA is a repressor enzyme (EC 3.4.21.88) that represses SOS response genes coding for DNA polymerases required for repairing DNA damage. LexA is intimately linked to RecA in the biochemical cycle of DNA damage and repair. RecA binds to DNA-bound LexA causing LexA to cleave itself in a process called autoproteolysis.

DNA damage can be inflicted by the action of antibiotics. Bacteria require topoisomerases such as DNA gyrase or topoisomerase IV for DNA replication. Antibiotics such as ciprofloxacin are able to prevent the action of these molecules by attaching themselves to the gyrase - DNA complex. This is counteracted by the polymerase repair molecules from the SOS response. Unfortunately the action is partly counterproductive because ciprofloxacin is also involved in the synthetic pathway to RecA type molecules which means that the bacteria responds to an antibiotic by starting to produce more repair proteins. These repair proteins can lead to eventual benevolent mutations which can render the bacteria resistant to ciprofloxacin.

  Mutations are traditionally thought of as happening as a random process and as a liability to the organism. Many strategies exist in a cell to curb the rate of mutations. Mutations on the other hand can also be part of a survival strategy. For the bacteria under attack from an antibiotic, mutations help to develop the right biochemistry needed for defense. Certain polymerases in the SOS pathway are error-prone in their copying of DNA which leads to mutations. While these mutations are often lethal to the cell, they can also lead to mutations which improve the bacteria's survival. In the specific case of topoisomerases, some bacteria have mutated one of their amino acids so that the ciproflaxin can only create a weak bond to the topoisomerase. This is one of the methods that bacteria use to become resistant to antibiotics.

  Impaired LexA proteolysis has been shown to interfere with ciprofloxacin ^.This offers potential for combination therapy that combine quinolones resistance. with strategies aimed at interfering with the action of LexA either directly, or via RecA.