..::Protein Data Bank (PDB)::..

Next Chapter, we will introduce you about PDB:>

  PROTEIN DATA BANK (PDB)

PDB - an introduction to a common term

» What is PDB?

1-The PDB is the Protein Data Bank, a single worlwide repository for 3D structural data of biological molecules.

2- 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.

>>How can PDB's be visualized?

Protein Data Bank files, containing some form of macromolecular coordinate set, are visualized via graphic computing. A myriad of advanced molecular visualization programs are used in academic and industrial setting, and some of these are specific to the field of research or the techniques used to collect the coordinate data. For example, X-ray crystallographers use O, XtalView, MAIN, or other programs for crystallographic modeling. These allow the researcher to model the coordinate set into the electron density from the collected X-ray data.
However, PDB files are "final" deposited coordinates. This means that the depositor has made their best effort to provide a final model that is as accurate as they could make it. Programs like Molscript, Pymol, SwissPDBview/DeepView, Molmol, SETOR, DINO and others are routinely used to visualize deposited coordinates.
In order to produce molecular graphics, one requires the following: graphics workstation computer, some form of molecular graphics software, and most importantly, training.
Symmation has been formally trained in X-ray crystallography and bioinformatics. We have the software and computer equipment, aside from our 8 years of experience. We are able to provide a complete solution to molecular graphics visualization that includes raw data interpretation, remodeling, refinement, structure analysis, and of course publication-quality graphics.
We can reduce your costs of operation, whatever sector you are in. Request information on PDB visualization and read our client testimonials that speak on our expertise!

 You may look at these three example below /(^_^)\ >

• Subtilisin
• Prolyl Aminopeptidase
• Lex A Repressor

Lets look at it,Jom!!

Subtilisin

The catalytic aspartate is protonated in the Michaelis complex formed between trypsin and an in vitro evolved substrate-like inhibitor: a refined mechanism of serine protease action.

The mechanism of serine proteases prominently illustrates how charged amino acid residues and proton transfer events facilitate enzyme catalysis. Here we present an ultrahigh resolution (0.93 Å) X-ray structure of a complex formed between trypsin and a canonical inhibitor acting... [ Read More & Search PubMed Abstracts ]
The mechanism of serine proteases prominently illustrates how charged amino acid residues and proton transfer events facilitate enzyme catalysis. Here we present an ultrahigh resolution (0.93 Å) X-ray structure of a complex formed between trypsin and a canonical inhibitor acting through a substrate-like mechanism. The electron density indicates the protonation state of all catalytic residues where the catalytic histidine is, as expected, in its neutral state prior to the acylation step by the catalytic serine. The carboxyl group of the catalytic aspartate displays an asymmetric electron density so that O?2-C? bond appears to be a double bond, with O?2 involved in a hydrogen bond to His-57 and Ser-214. Only when Asp-102 is protonated on O?1 atom a DFT simulation could reproduce the observed electron density. The presence of a putative hydrogen atom is also confirmed by a residual mFobs-DFcalc density above 2.5 ? next to O?1. As a possible functional role for the neutral aspartate in the active site, we propose that in the substrate bound form the neutral aspartate residue helps to keep the pKa of the histidine sufficiently low, in the active neutral form. When the histidine receives a proton during the catalytic cycle, the aspartate becomes simultaneously negatively charged providing additional stabilization for the protonated histidine and indirectly to the tetrahedral intermediate. This novel proposal unifies the seemingly conflicting experimental observations, which were previously seen as either supporting the charge relay mechanism or the neutral-pKa histidine theory.

Prolyl peptidase

The structural basis for catalysis and specificity of the X-prolyl dipeptidyl aminopeptidase from Lactococcus lactis.

Rigolet, P.,   Mechin, I.,   Delage, M.M.,   Chich, J.F.

PubMed Abstract:
The X-prolyl dipeptidyl aminopeptidase (X-PDAP) from Lactococcus lactis is a dimeric enzyme catalyzing the removal of Xaa-Pro dipeptides from the N terminus of peptides. The structure of the enzyme was solved at 2.2 A resolution and provides a model for... [ Read More & Search PubMed Abstracts ]
The X-prolyl dipeptidyl aminopeptidase (X-PDAP) from Lactococcus lactis is a dimeric enzyme catalyzing the removal of Xaa-Pro dipeptides from the N terminus of peptides. The structure of the enzyme was solved at 2.2 A resolution and provides a model for the peptidase family S15. Each monomer is composed of four domains. The larger one presents an alpha/beta hydrolase fold and comprises the active site serine. The specificity pocket is mainly built by residues from a small helical domain which is, together with the N-terminal domain, essential for dimerization. A C-terminal moiety probably plays a role in the tropism of X-PDAP toward the cellular membrane. These results give new insights for further exploration of the role of the enzymes of the SC clan.

 

Lex A Repressor

Repressor LexA or LexA is a repressor enzymeEC 3.4.21.88) that represses SOS response genesDNA 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. ( coding for

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 resistance.This offers potential for combination therapy that combine quinolones with strategies aimed at interfering with the action of LexA either directly, or via RecA.

That's all from helpless me.Do comment if you like to..=)