Go to the abstract in the NAR 2002 Database Issue.
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New England Biolabs 32 Tozer Rd. Beverly, MA 01915, USA
Contact perler@neb.com
Inteins are self-catalytic protein splicing elements that interrupt host proteins, called exteins. Extein ligation to form a native peptide bond and the presence of conserved intein motifs differentiate intein-mediated protein splicing from other post-translational processing events. InBase, the intein Database and Registry, is a curated compilation of published and unpublished information about protein splicing. Since few textbooks cover protein splicing, InBase provides background material suitable for classroom use. At the same time, detailed information is presented in a layered format with general discussions and tables pointing to more specific data, such as the protein splicing mechanism, organism data, motif sequences, proximal insertion site sequences, selected properties and intein alleles. Individual intein records contain detailed information about each intein, including the amino acid sequence, size, insertion site sequence data, comments on unusual properties, presence of endonuclease domains or activity, submitter contact information, host organism, host protein, and a reference list for each intein. Section 5 describes the criteria for intein identification, including a description of conserved motifs and polymorphisms. The bibliography includes annotations for reviews, application papers, related papers and recent papers. PubMed hot links allow the reader to retrieve abstracts from the National Library of Medicine. An intein-specific BLAST server is now available to assist in identifying new inteins. Since inteins are predominantly found in extein active sites and cofactor or substrate binding pockets, identification of inteins can potentially help locate these elements in uncharacterized proteins. Intein data can be submitted confidentially or for immediate release using the on-line Submission Form or by email.
The InBase home page has been reorganized to move background information into a separate section called Intein Basics. An intein-specific BLAST server is now available and the amino acid sequence is present in individual intein pages. A new splicing mechanism for inteins lacking an N-terminal nucleophile has been included in the Splicing Mechanism section. The first crystal structure of an intein precursor shed light onto the amino acids that assist catalysis and the need for conformational changes to align nucleophiles during the sequential steps in the protein splicing pathway. Numerous protein engineering applications take advantage of the C-terminal alpha-thioester formed on target proteins purified from intein vectors, such as the commercially available IMPACTô system (NEB).
I am grateful to my coworkers at NEB, Ellen M. Lambrinos and Ching Lin for help in maintaining InBase, Janos Posfai and Tamas Vincze for developing and maintaining the InBase BLAST server, and to all the intein workers who have submitted their published and unpublished data, especially Shmuel Pietrokovski.
Category Protein Databases
Go to the abstract in the NAR 2002 Database Issue.