Protein structure entries

Figure 7-16. Superimpasition of the X-ray structure of the tetracycline repressor class D dimer (dark, protein database entry 2TRT) with the calculated geometrical average of a 3 ns MD simulation (light trace). Only the protein backbone C trace Is shown, The secondary structure elements and the tertiary structure are almost perfectly reproduced and maintained throughout the whole production phase of the calculation,...

Due to the ready accessibility of SH2 domains by molecular biology techniques, numerous experimentally determined 3D structures of SH2 domains derived by X-ray crystallography as well as heteronuclear multidimensional NMR spectroscopy are known today. The current version of the protein structure database, accessible to the scientific community by, e.g., the Internet (http //www.rcsb.org/pdb/) contains around 80 entries of SH2 domain structures and complexes thereof. Today, the SH2 domain structures of Hck [62], Src [63-66], Abl [67], Grb2 [68-71], Syp [72], PLCy [73], Fyn [74], SAP [75], Lck [76,77], the C- and N-terminal SH2 domain ofp85a [78-80], and of the tandem SH2 domains Syk [81,82], ZAP70 [83,84], and SHP-2 [85] are determined. All SH2 domains display a conserved 3D structure as can be expected from multiple sequence alignments (Fig. 4). The common structural fold consists of a central three-stranded antiparallel ft sheet that is occasionally extended by one to three additional short strands (Fig. 5). This central ft sheet forms the spine of the domain which is flanked on both sides by regular a helices [49, 50,60]. 

Fig. 6. Schematic diagram of the peptide-protein interaction mode as seen in the crystallo-graphically refined structured of the Lck SH2 domain-peptide complex, Protein Databank entry code 1 LKK.PDB. The residues directly engaged in intramolecular hydrogen bonds (dotted lines) are labeled explicitly... 

Determination of three-dimensional protein structures has become an important tool in protein research, indicated by the exponentially growing number of protein data bank entries during the last decade. They have contributed considerably to our understanding of function and mechanism of biomolecules. Structures of proteins alone or in complex with their substrates or binding partners like cofactors, DNA, or other proteins can visualize interactions at the atom-... 

Prosite is perhaps the best known of the domain databases (Hofmann et al., 1999). The Prosite database is a good source of high quality annotation for protein domain families. Prosite documentation includes a section on the functional meaning of a match to the entry and a list of example members of the family. Prosite documentation also includes literature references and cross links to other databases such as the PDB collection of protein structures (Bernstein et al., 1977). For each Prosite document, there is a Prosite pattern, profile, or both to detect the domain family. The profiles are the most sensitive detection method in Prosite. The Prosite profiles provide Zscores for matches allowing statistical evaluation of the match to a new protein. Profiles are now available for many of the common protein domains. Prosite profiles use the generalized profile software (Bucher et al., 1996). 

Selected entries from Methods in Enzymology [vol, page(s)] Acquisition of frequency-discriminated spectrum, 239, 162-166, 170 sensitivity, 239, 169-173 constant-time, 239, 23-26 doublequantum filtered, 239, 236 gradient pulse experiments, 239, 185-189 protein structural information, 239, 377-379 pulse sequence and coherence transfer pathway, 239, 148-149 paramagnetic metalloprotein, 239, 494-497 data recording, SWAT method, 239, 166-169, 172 line shapes, effects of gradient pulses, 239, 162-166 identification of protein amino acid resonances, 232, 100 cyclosporin A, 239, 240-241. 

Based on an analysis of the protein data bank (Berman et at, 2000) January 2005, the entries considered for the virus column were selected as containing virus in the PDB header and manually checked to eliminate component proteins and duplicates, the total column represents all crystal structure entries then in the PDB, including viruses and proteins. 

Currently, only a handful of examples of unique protein carboxylate-zinc interactions are available in the Brookhaven Protein Data Bank. Each of these entries, however, displays syn coordination stereochemistry, and two are bidentate (Christianson and Alexander, 1989) (Fig. 5). Other protein structures have been reported with iyw-oriented car-boxylate-zinc interactions, but full coordinate sets are not yet available [e.g., DNA polymerase (Ollis etal., 1985) and alkaline phosphatase (Kim and Wyckoff, 1989)]. A survey of all protein-metal ion interactions reveals that jyw-carboxylate—metal ion stereochemistry is preferred (Chakrabarti, 1990a). It is been suggested that potent zinc enzyme inhibition arises from syn-oriented interactions between inhibitor carboxylates and active-site zinc ions (Christianson and Lipscomb, 1988a see also Monzingo and Matthews, 1984), and the structures of such interactions may sample the reaction coordinate for enzymatic catalysis in certain systems (Christianson and Lipscomb, 1987). 

AMINO ACIDS. The scores of proteins which make up about one-half of the dry weight of the human body and that are so vital to life functions are made up of a number of amino adds in various combinations and configurations. The manner in which the complex protein structures are assembled from amino acids is described in the entry on Ihotcin. For some useis of tills book, it may be helpful to scan that portion of the piotein entry that deals with the chemical nature of proteins prior to considering the details of this immediate entry on amino acids. 

The size of the PDB is increasing very rapidly in the January 1994 full release of the databank there were 2327 coordinate entries of which 605 had appeared since the previous, October 1993, release. The entries comprise 2143 protein structures, together with 156 DNA, 18 RNA and 10 carbohydrate structures. The PDB also contains bibliographic references to more than 100 maeromolecular structures which have been published, but which have not been deposited in the PDB by the authors. Recently there has been strong pressure on journals to make deposition of coordinates in the PDB a condition of publication [31]. 

The Sequence Retrieval System (Etzold et ah, 1996) is a network browser for databases at EBI. The system allows users to retrieve, link, and access entries from all the interconnected resources such as nucleic acid, EST, protein sequence, protein pattern, protein structure, specialist/boutique, and/or bibliographic databases. The SRS is also a database browser of DDBJ, ExPASy, and a number of servers as the query system. The SRS can be accessed from EBI Tools server at http // www2.ebi.ac.uk/Tools/index.html or directly at http //srs6.ebi.ac.uk/. The SRS permits users to formulate queries across a range of different database types via a single interface in three different methods (Figure 3.4) ... 

EMBL Nucleotide Sequence Database. SWISS-PROT consists of core sequence data with minimal redundancy, citation and extensive annotations including protein function, post-translational modifications, domain sites, protein structural information, diseases associated with protein deficiencies and variants. SWISS-PROT and TrEMBL are available at EBI site, http //www.ebi.ac.uk/swissprot/, and ExPASy site, http //www.expasy.ch/sprot/. From the SWISS-PROT and TrEMBL page of ExPASy site, click Full text search (under Access to SWISS-PROT and TrEMBL) to open the search page (Figure 11.3). Enter the keyword string (use Boolean expression if required), check SWISS-PROT box, and click the Submit button. Select the desired entry from the returned list to view the annotated sequence data in Swiss-Prot format. An output in the fasta format can be requested. Links to BLAST, feature table, some ExPASy proteomic tools (e.g., Compute pI/Mw, ProtParam, ProfileScan, ProtScale, PeptideMass, ScanProsite), and structure (SWISS-MODEL) are provided on the page. 

The UniProt KB is an automatically and manually annotated protein database drawn from translation of DDBJ/EMBL-Bank/GenBank coding sequences and directly sequenced proteins. Each sequence receives a imique, stable identifier allowing unambiguous identification of any protein across datasets. The KB also provides cross-references to external data collections such as the underlying DNA sequence entries in the DDBJ/EMBL-Bank/GenBank nucleotide sequence databases, 2D PAGE and 3D protein structure databases, various protein domain... 

Estradiol is the natural agonist ligand of the estrogen receptors (ER). There are two isotypes of the estrogen receptor, ER-a and ER-y . There are four structures of the complex between the LED of ER-a and estradiol in the PBD. Expression, purification and crystallization of LEDs can often be problematic. Thus, the first structure solved (PDE entry lERE) [6] used protein in which the free cysteines were carboxymethylated. The refined structure showed at least one of the cysteines was modified. Another structure (PDE entry 1A52) [7] used protein that was refolded. The structure of this protein showed an artifact where two LEDs were connected by an intermolecular disulfide bond. Through much experimentation, conditions were found to express, purify and crystallize ER-a LED without modification or refolding. The protein structure was deposited as PDB entry IQKU [8] and it is this protein structure that will be discussed. 

Every second protein domain in PDB is represented by more than one PDB entry 20% of proteins have two structures, and the remaining 30% more than two structures. Some of them are mutants (e.g., 400 of T4 lysozyme structures from Brian Matthews s laboratory) but in most cases, these multiple structures represent snapshots of the pocket conformational diversity. Furthermore, many entries contain more than one chain in an asymmetric unit. These protein structures related by noncrystallographic symmetry can also be used as a source of multiple pocket conformations. The noncrystallographic symmetry-related subunits increase the number of domains already represented by multiple experimental conformations from 50% to the overall level of 75% (Fig. 2). About 5% of the domains are represented by more than 30 copies. 

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