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Monday, January 3, 2011

PROTEIN DATA BANK

The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. (See also crystallographic database). The data, typically obtained by X-ray crystallography or NMR spectroscopybiologists 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
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; GO categorize structures based on genes.

The PDB originated as a grassroots effort.In 1971, Walter Hamilton of the Brookhaven National Laboratory agreed to set up the data bank at Brookhaven. Upon Hamilton's death in 1973, Tom Koeztle took over direction of the PDB. In January 1994, Joel Sussman was appointed head of the PDB. In October 1998,[2] the PDB was transferred to the Research Collaboratory for Structural Bioinformatics (RCSB); the transfer was completed in June 1999. The new director was Helen M. Berman of Rutgers University (one of the member institutions of the RCSB).[3] In 2003, with the formation of the wwPDB, the PDB became an international organization. The founding members are PDBe (Europe), RCSB(USA), and PDBj (Japan). The BMRB joined in 2006. Each of the four members of wwPDB can act as deposition, data processing and distribution centers for PDB data. The data processing refers to the fact that wwPDB staff review and annotates each submitted entry. The data are then automatically checked for plausibility. (The source code for this validation software has been made available to the public at no charge.

The file format initially used by the PDB was called the PDB file format. This original format was restricted by the width of computer punch cards to 80 characters per line. Around 1996, the "macromolecular Crystallographic Information file" format, mmCIF, started to be phased in. An XML version of this format, called PDBML, was described in 2005.The structure files can be downloaded in any of these three formats. In fact, individual files are easily downloaded into graphics packages using web addresses:
  • For PDB format files, use, e.g., http://www.pdb.org/pdb/files/4hhb.pdb.gz or http://pdbe.org/download/4hhb
  • For PDBML (XML) files, use, e.g., http://www.pdb.org/pdb/files/4hhb.xml.gz or http://pdbe.org/pdbml/4hhb
The "4hhb" is the PDB identifier. Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. (This cannot be used as an identifier for biomolecules, because often several structures for the same molecule—in different environments or conformations—are contained in PDB with different PDB IDs.)


HtrA 
H198P/T167V DOUBLE MUTANT OF DEGS-DELTAPDZ PROTEASE


Primary Citation
Allostery is an intrinsic property of the protease domain of DegS: implications for enzyme function and evolution.
Sohn, J.,   Grant, R.A.,   Sauer, R.T.
Journal: (2010) J.Biol.Chem. 285: 34039-34047
PubMed: 20739286  
PubMedCentral: PMC2962503  
DOI: 10.1074/jbc.M110.135541  
Search Related Articles in PubMed  
PubMed Abstract:
DegS is a periplasmic Escherichia coli protease, which functions as a trimer to catalyze the initial rate-limiting 
step in a proteolytic cascade that ultimately activates transcription of stress response genes in the cytoplasm. 
Each DegS subunit consists of a proteas.












  • Molecule:Protease degS
    Polymer:1Type:polypeptide(L)Length:241
    Chains:A
    EC#:3.4.21.-    
    Fragment:protease domain


    Classification: Hydrolase
    Structure Weight: 25847.40






















































LonA
CRYSTAL STRUCTURE OF BACILLUS SUBTILIS LON N-TEMINAL DOMAIN


Primary Citation
Crystal structures of Bacillus subtilis Lon protease.
Duman, R.E.,   Lowe, J.
Journal: (2010) J.Mol.Biol. 401: 653-670
PubMed: 20600124  
DOI: 10.1016/j.jmb.2010.06.030  
Search Related Articles in PubMed  
PubMed Abstract:
Lon ATP-dependent proteases are key components of the protein quality control systems of bacterial cells
and eukaryotic organelles. Eubacterial Lon proteases contain an N-terminal domain, 
an ATPase domain, and a protease domain, all in one polypeptide chain. The N-terminal domain.
  •   Molecular Description
    Classification: Hydrolase
    Structure Weight: 48027.40



    Molecule:ATP-dependent protease La 1
    Polymer:1Type:polypeptide(L)Length:209
    Chains:A, B
    EC#:3.4.21.53    
    Fragment:BsLon, N-terminal domain















    CipP
STRUCTURE OF CIpP FROM BACILLUS SUBTILIS IN MONOCLINIC CRYSTAL FORM

Primary Citation
Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism.
Lee, B.-G.,   Park, E.Y.,   Lee, K.-E.,   Jeon, H.,   Sung, K.H.,   Paulsen, H.,   Rubsamen-Schaeff, H.,   Brotz-Oesterhelt, H.,   Song, H.K.
Journal: (2010) Nat.Struct.Mol.Biol. 17: 471-478
PubMed: 20305655  
DOI: 10.1038/nsmb.1787  
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PubMed Abstract:
Clp-family proteins are prototypes for studying the mechanism of ATP-dependent proteases because the proteolytic activity of the ClpP core is tightly regulated by activating Clp-ATPases. Nonetheless, the proteolytic activation mechanism has remained elusive because of the lack of a complex.
  •   Molecular Description

    Classification: Hydrolase
    Structure Weight: 154303.80



    Molecule:ATP-dependent Clp protease proteolytic subunit
    Polymer:1Type:polypeptide(L)Length:199
    Chains:A, B, C, D, E, F, G
    EC#:3.4.21.92    
    Mutation:T193L,D195H,K196H,K19

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