Words similar to thermus
Example sentences for: thermus
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Using the experimentally determined structure as a guide, we split the β and β' subunits of the Thermus thermophilus DDRP and the largest two subunits of the yeast DDRP into individual globular domains and investigated them by visual inspection of the topology, structural searches of the PDB database using the DALI program and iterative searches of the NR database using PSI-BLAST.
The β' subunit of bacterial DDRPs contains a single Zn-ribbon at the N-terminus (region 56-81 of Thermus β' subunit; Fig.
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.
A search of the PDB database using the DALI program [ 61 ] , with this β-barrel from Thermus thermophilus β' subunit submitted as a query (pdb: 1iw7, chain D region: 625-749), retrieved the N-terminal domain of the CDC48-like AAA ATPases, formate dehydrogenases, aspartate decarboxylases and Barwin.
In addition to the SBHMs that are conserved among all bacterial lineages, a cassette of up to four SBHMs are present N-terminal of the DPBB domain in the β' subunit of Thermus , Deinococcus and Thermotoga (Fig.
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