Introduction to PDB
The PDB is the Protein Data Bank, a single worlwide repository for 3D structural data of biological molecules. A PDB is a file, typically with a "pdb" file extension, contains 3D structural data of a particular biological molecule. In short, a PDB file is broken into two sections:
(i) a header that contains much background information on the molecule in question such as authors and experimental conditions,
(ii) 3D coordinate data that contain the vital experimental data in the form of 3D cartesian coordinates, B-factors, atom information, and more.
The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins, viruses and nucleic acids.. The data are available to the public and typically obtained by X-ray crystallography (80%)or NMR spectroscopy (16%) and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, andRCSB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.
The PDB is a key resource in areas of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, such as the NIH in the USA, now require scientists to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived (i.e., secondary) databases that categorize the data differently. For example, both SCOP andCATH categorize structures according to type of structure and assumed evolutionary relations; GO categorize structures based on genes.
PDB was founded in 1971 by Brookhaven National Laboratory, New York. First set of data were entered on punched cards. Then with magnetic tapes. It was then transferred to the Research Collaborators for Structural Bioinformatics (RCSB) in 1998. Currently it holds 29,000 released structures and it is an important resource for research in the academic, pharmaceutical, and biotechnology sectors such as to know that will this molecule turns into a cancer cell? Can this combination of molecules cure common cold? How does radiation affect the RNA and DNA?
STRUCTURES:
1) Crystallographic analysis of counter-ion effect on Subtilisin enzymatic action in Acetonitrile
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| Display: Ball & Stick, Colour: CPK |
Experimented Method:
Many bacterial pathogens produce extracellular proteases that degrade the extracellular matrix of the host and therefore are involved in disease pathogenesis. Dichelobacter nodosus is the causative agent of ovine footrot, a highly contagious disease that is characterized by the separation of the hoof from the underlying tissue. D. nodosus secretes three subtilisin-like proteases whose analysis forms the basis of diagnostic tests that differentiate between virulent and benign strains and have been postulated to play a role in virulence. We have constructed protease mutants of D. nodosus; their analysis in a sheep virulence model revealed that one of these enzymes, AprV2, was required for virulence. These studies challenge the previous hypothesis that the elastase activity of AprV2 is important for disease progression, since aprV2 mutants were virulent when complemented with aprB2, which encodes a variant that has impaired elastase activity. We have determined the crystal structures of both AprV2 and AprB2 and characterized the biological activity of these enzymes. These data reveal that an unusual extended disulphide-tethered loop functions as an exosite, mediating effective enzyme-substrate interactions. The disulphide bond and Tyr92, which was located at the exposed end of the loop, were functionally important. Bioinformatic analyses suggested that other pathogenic bacteria may have proteases that utilize a similar mechanism. In conclusion, we have used an integrated multidisciplinary combination of bacterial genetics, whole animal virulence trials in the original host, biochemical studies, and comprehensive aof crystal structures to provide the first definitive evidence that the extracellular secreted proteases produced by D. nodosus are required for virulence and to elucidate the molecular mechanism by which these proteases bind to their natural substrates. We postulate that this exosite mechanism may be used by proteases produced by other bacterial pathogens of both humans and animals.
| Experiment method | X-RAY DIFFRACTION with resolution of 2.24 Å |
| Authors | Cianci, M., Tomaszewski, B., Helliwell, J.R., Halling, P.J. |
| Classification | Hydrolase |
2) Structure of human cytosolic X-prolyl aminopeptidase
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| Display: Ribbons, Colour: Temperature |
DETAILS
Experiment methods:
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 sarcosineresidues 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 anunusual extra space at the bottom of the hydrophobic pocket where proline residue is fixed in the prolyl aminopeptidase. Moreover, 4-acetyloxyproline-betaNA (4-acetyloxyprolinebeta-naphthylamide) was a 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 involvedsignificantly 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 acetylation process by the bacteria.
| Experiment method | X-RAY DIFFRACTION with resolution of 1.60 Å |
| Authors | Li, X., Lou, Z., Rao, Z. |
| Classification | Hydrolase |
3) Human START domain of Acyl-coenzyme A thioesterase 11 (ACOT11)
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Display: Wireframe, Colour: Shapely |
Experiment methods :
Escherichia coli shows a pleiotropic response (the SOS response) to treatments that damage DNA or inhibit DNA replication. Previous evidence has suggested that the product of the lexA gene is involved in regulating the SOS response, perhaps as a repressor, and that it is sensitive to the recA protease. We show here that lexA protein is a repressor of at least two genes, recA and lexA. Purified protein bound specifically to the regulatory regions of the two genes, as judged by DNase I protection experiments, and it specifically inhibited in vitro transcription of both genes. The binding sites in recA and lexA were found to be about 20 base pairs (bp) and 40 bp long, respectively. The 40-bp sequence in lexA was composed of two adjacent 20-bp sequences, which had considerable homology to one another and to the corresponding recA sequence. These 20-bp sequences, which we term "SOS boxes," show considerable inverted repeat structure as well. These features suggest that each box represents a single repressor binding site. Finally, we found that purified lexA protein was a substrate for the recA protease in a reaction requiring ATP or an analogue, adenosine 5'-[gamma-thio]triphosphate, and denatured DNA.
| Experiment method | X-RAY DIFFRACTION with resolution of 2.00 Å |
| Authors | Siponen, M.I., Lehtio, L., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Thorsell, A.G., Tresaugues, L., Van-Den-Berg, S., Weigelt, J., Welin, M., Wikstrom, M., Wisniewska, M., Shueler, H., Structural Genomics Consortium (SGC) |
| Classification | Lipid Transport |
All the structure of protein above are modified using the RasWin software where all the date has been taken from the link: RCSB
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