6SBS

YtrA from Sulfolobus acidocaldarius, a GntR-family transcription factor

Summary for 6SBS

• Entry DOI: 10.2210/pdb6sbs/pdb
• Descriptor: Regulatory protein (2 entities in total)
• Functional Keywords: transcription regulation, archaea, sulfolobus, gntr, ytra, transcription
• Biological source: Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)
• Total number of polymer chains: 2
• Total formula weight: 27810.49

Authors

Lemmens, L.,Valegard, K.,Lindas, A.C.,Peeters, E.,Maes, D. (deposition date: 2019-07-22, release date: 2019-07-31, Last modification date: 2024-05-15)

Primary citation

Lemmens, L.,Tilleman, L.,De Koning, E.,Valegard, K.,Lindas, A.C.,Van Nieuwerburgh, F.,Maes, D.,Peeters, E.
YtrASa, a GntR-Family Transcription Factor, Represses Two Genetic Loci Encoding Membrane Proteins inSulfolobus acidocaldarius.
Front Microbiol, 10:2084-2084, 2019

PubMed Abstract: In bacteria, the GntR family is a widespread family of transcription factors responsible for the regulation of a myriad of biological processes. In contrast, despite their occurrence in archaea only a little information is available on the function of GntR-like transcription factors in this domain of life. The thermoacidophilic crenarchaeon harbors a GntR-like regulator belonging to the YtrA subfamily, encoded as the first gene in an operon with a second gene encoding a putative membrane protein. Here, we present a detailed characterization of this regulator, named YtrA, with a focus on regulon determination and mechanistic analysis with regards to DNA binding. Genome-wide chromatin immunoprecipitation and transcriptome experiments, the latter employing a overexpression strain, demonstrate that the regulator acts as a repressor on a very restricted regulon, consisting of only two targets including the operon encoding its own gene and a distinct genetic locus encoding another putative membrane protein. For both targets, a conserved 14-bp semi-palindromic binding motif was delineated that covers the transcriptional start site and that is surrounded by additional half-site motifs. The crystallographic structure of YtrA was determined, revealing a compact dimeric structure in which the DNA-binding motifs are oriented ideally to enable a specific high-affinity interaction with the core binding motif. This study provides new insights into the functioning of a YtrA-like regulator in the archaeal domain of life.

PubMed: 31552000
DOI: 10.3389/fmicb.2019.02084

Experimental method

X-RAY DIFFRACTION (2.801 Å)