SCOP: a Structural Classification of Proteins database

Abstract

The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. The database can be used as a source of data to calibrate sequence search algorithms and for the generation of population statistics on protein structures. The database and its associated files are freely accessible from a number of WWW sites mirrored from URL http://scop. mrc-lmb.cam.ac.uk/scop/

The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences

“…These searches were performed by means of the genome assignment server SUPERFAMILY [21] that contains a library of hidden Markov models (HMMs) and the results of searches by these models against completely sequenced genomes. The HMMs of SUPERFAMILY are based on the sequences of domains collected in the Structural Classification of Proteins (SCOP) database [47] and are thus applicable for a structural classification of proteins. The search for corynebacterial DNA-binding proteins also included information deduced from the respective genome annotations deposited in public databases [12-14].…”

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“…Protein structures can be divided into four major structural classes, according to their secondary structure content and arrangement (SCOP [11]). There are two homogeneous classes and two heterogeneous classes.…”

“…The two heterogeneous classes comprise both alpha helices and beta strands. The alpha/beta class consists of mainly parallel beta sheets (beta-alpha-beta units), and the alpha+beta class that consists of mainly antiparallel beta sheets (segregated alpha and beta regions) [11]. Each class obviously differs in its secondary structure content.…”

Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding

“…Both proteins have now been classified by SCOP (Hubbard et al, 1999) as being members of a novel Sfri0576-like family which belongs to the SpoIIAA superfamily. However, despite sharing the same fold, their structures differ significantly in the relative disposition of two surface -helices and in their mode of dimerization.…”