The Protein Data Bank (PDB) archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
The data, typically obtained by X-ray crystallography
or NMR spectroscopy
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
, and RCSB). 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 and CATH categorize structures according to type of structure and assumed evolutionary relations.
SUBTILISIN
Enoyl-[acyl-carrier-protein] reductase
Molecule : [NADPH]
Polymer : 1
Type : polypeptide(L)
Length : 258
Chains : A,D
Scientific name : BAcillus subtilis
Expression System : Escherichnia coli
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 nucleophilic attack on the peptide (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. 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.
PROLYL AMINOPEPTIDASE
Classification: Hydrolase
Structure Weight : 29320.31
Molecule : SUBTILISIN CARLSBERGH
Polymer : 1
Type : polypeptide (L)
Length : 274
Chains : A
Fragment : RESIDUES 106-379
Scientific Name : Bacillus licheniformis
| Journal: (2010) J.Am.Chem.Soc. 132: 2293-2300
PubMed: 20099851
DOI: 10.1021/ja908703c
When enzymes are in low dielectric nonaqueous media, it would be expected that their charged groups would be more closely associated with counterions. There is evidence that these counterions may then affect enzymatic activity. In this paper, the placement of several Cs(+) and Cl(-) ions in crystals of the serine protease subtilisin Carlsberg is presented. Ions are more readily identified crystallographically through their anomalous diffraction using softer X-rays. The protein conformation is very similar to that of the enzyme without CsCl in acetonitrile, both for the previously reported ( 1SCB ) and our own newly determined model. No fewer than 11 defined sites for Cs(+) cations and 8 Cl(-) anions are identified around the protein molecule, although most of these have partial occupancy and may represent nonspecific binding sites.The active site appears only minimally sterically perturbed by the ion presence around it, so alternative activation mechanisms can be suggested: an electrostatic redistribution and/or a larger hydration sphere that enhances the protein domain.
|
|
|
|
|
|
LEX A REPRESSOR
Classification : Lipid Transport
Structure Weight : 60191.69
Molecule : Thioesterase, adipose associated, isoform BFIT2
Polymer : 1
Type : polypeptide(L)
length : 258
Chains : A,B
Fragment : STARTdomain, UNP residues 339-594
Scientific Name : Homo Sapiens
Common name : Human expression
System : Escherichia coli
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.
