Characterization of the TrmB‐like protein, PF0124, a TGM‐recognizing global transcriptional regulator of the hyperthermophilic archaeon <i>Pyrococcus furiosus</i>

Lee, Sung–Jae; Surma, Melanie; Seitz, Sabine; Hausner, Winfried; Thomm, Michael; Boos, Winfried

doi:10.1111/j.1365-2958.2007.05780.x

Cited by 31 publications

(61 citation statements)

References 33 publications

(48 reference statements)

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“…Depending on its position within the respective promoter, Tgr binds to it, acting as an activator when present upstream of BRE/TATA box of genes encoding gluconeogenic proteins but as a repressor when positioned downstream of the BRE/ TATA box of genes encoding glycolytic genes. TrmBL1 of P. furiosus showing 67% sequence identity to Tgr and exhibits the same function as Tgr [3].…”

Section: Introductionmentioning

confidence: 94%

“…Nevertheless, when tested by band shift analysis and run-off transcription assays, it was found that TrmBL2 was able to recognize the MD promoter but no obvious pattern with respect to other TGM-containing promoters could be detected, neither could a specific DNA sequence motif for TrmBL2 be identified [3,5].…”

Section: Introductionmentioning

confidence: 97%

“…Sequence alignment of the TrmB family of proteins revealed that TrmBL2 lacks the C-terminal sugar-binding subdomain present in other TrmB orthologs [3,5]. Nevertheless, when tested by band shift analysis and run-off transcription assays, it was found that TrmBL2 was able to recognize the MD promoter but no obvious pattern with respect to other TGM-containing promoters could be detected, neither could a specific DNA sequence motif for TrmBL2 be identified [3,5].…”

Section: Introductionmentioning

confidence: 98%

“…The early search for homologs of TrmB within four members of the Thermococcales showed a series of five proteins named TrmBL1, TrmBL2, TrmBL3 and TrmBL4 [3,4]. These sequences showed a considerable degree of sequence identity at the N-terminus overlapping the ewHTH motif seen in the crystal structure of TrmB.…”

Section: Introductionmentioning

confidence: 99%

“…Apart from TrmBL2, not all TrmB members are present in all four Thermococcales. A recent review discusses the now large TrmB family recognized in the archaea [3,5].…”

Section: Introductionmentioning

confidence: 99%

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Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein

Ahmad

Waege

Hausner

et al. 2015

Journal of Molecular Biology

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The crystal structure of TrmBL2 from the archaeon Pyrococcus furiosus shows an association of two pseudosymmetric dimers. The dimers follow the prototypical design of known bacterial repressors with two helix-turn-helix (HTH) domains binding to successive major grooves of the DNA. However, in TrmBL2, the two dimers are arranged at a mutual displacement of approximately 2 bp so that they associate with the DNA along the double-helical axis at an angle of approximately 80°.While the deoxyribose phosphate groups of the double-stranded DNA (dsDNA) used for co-crystallization are clearly seen in the electron density map, most of the nucleobases are averaged out. Refinement required to assume a superposition of at least three mutually displaced dsDNAs. The HTH domains interact primarily with the deoxyribose phosphate groups and polar interactions with the nucleobases are almost absent.This hitherto unseen mode of DNA binding by TrmBL2 seems to arise from nonoptimal protein-DNA contacts made by its four HTH domains resulting in a low-affinity, nonspecific binding to DNA.

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Section: Introductionmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

“…Apart from TrmBL2, not all TrmB members are present in all four Thermococcales. A recent review discusses the now large TrmB family recognized in the archaea [3,5].…”

Section: Introductionmentioning

confidence: 99%

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