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Example sentences for: scop
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Whereas other resources are limited to what is present in PDB or SCOP, PAT provides additional domains from PDP, and genetic domains from Astral.
The DSBH fold that comprises the core domain of the 2OG-Fe(II) dioxygenases is also present in a large number of proteins typified by the arabinose-binding domain of the transcription regulator AraC, plant seed proteins such as vicilin, and oxalate oxidase ([ 29]; see SCOP [ 12]).
Visual examination of the structure of this insert domain revealed a topology with elements of both a sandwich and a barrel, and two "waist"-like structures that are characteristic of the sandwich-barrel hybrid motif (SBHM) fold [ 75 76 ] (see also the SCOP database [ 65 ] ). The SBHM fold is present in biotin/lipoate carrier domains and their homologs found in a variety of enzymes and transporters [ 76 ] . A DALI search with this insert domain from the β subunit of Thermus DDRP showed similarity to the SBHMs from various biotin/lipoate-binding enzymes, such as acetyl-CoA carboxylase (1bdo) or dihydrolipoamide acetyltransferase (1iyu) with Z scores of ~6 and RMSD ~2.
The region of structural similarity shared by the catalytic domain of the β' subunit of the DDRPs and the above proteins corresponds to a distinct globular fold known as the double-psi beta-barrel (DPBB) [ 62 63 64 ] . The SCOP database included the RNA polymerase subunits in the multidomain protein class but mentions the presence of a DPBB domain in each of the β and β' subunits ( [ 65 ] ; see below).
The APEs, DNase-1 and inositol 5'-polyphosphate phosphatases (IPP) have been grouped according to the SCOP database [ 30 ] as the DNase-1 like superfamily.
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