Structure of a conserved CoA-binding protein synthesized by a cell-free system

Wada, Takashi; Shirouzu, Mikako; Terada, Takaho; Ishizuka, Yoshiko; Matsuda, Takayoshi; Kigawa, T.; Kuramitsu, Seiki; Park, Sam Yong; Tame, J.R.H.; Yokoyama, Shigeyuki

doi:10.1107/s0907444903010515

Cited by 18 publications

(10 citation statements)

References 20 publications

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“…In order to determine the RNAP-binding ability of T. thermophilus E , the sigE gene was cloned and expressed in an E. coli cell-free system (12,31) in the absence or presence of the T. thermophilus RNAP core enzyme (Fig. 3).…”

Section: With the Combination Of In Vitro Transcription Assay And Genmentioning

confidence: 99%

Identification of Promoters Recognized by RNA Polymerase-σ ^E Holoenzyme from Thermus thermophilus HB8

et al. 2007

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Thermus thermophilusE , an extracytoplasmic function factor from the extremely thermophilic bacterium Thermus thermophilus HB8, bound to the RNA polymerase core enzyme and showed transcriptional activity. With the combination of in vitro transcription assay and GeneChip technology, we identified three promoters recognized by E . The predicted consensus promoter sequence for E is 5-CA(A/T)(A/C)C(A/C)-N 15 -CCGTA-3.Bacterial DNA-dependent RNA polymerase (RNAP) is composed of a core enzyme with the subunit structure ␣ 2 ␤␤Ј and a subunit that is responsible for promoter recognition (3,5,26). In general, most transcription in exponentially growing cells is initiated by an RNAP holoenzyme containing a housekeeping factor, a homolog of Escherichia coli 70 . In contrast, alternative factors are involved in the transcription of specialized genes such as those that are activated under specific stress conditions and during growth transitions and morphological changes and those involved in pathogens (1,6,9,11,17,21).Most alternative factors, i.e., other than the 54 family, are related in sequence to members of the housekeeping 70 family, and they have been divided into three groups based on phylogenetic relatedness (9, 15, 16). Group 4 factors, also called extracytoplasmic function (ECF) factors, are distant, according to sequence similarity, from the 70 family, and their sequences are divergent relative to those of most other factors. While a typical 70 -type (e.g., group 1) factor consists of four regions, a typical ECF factor consists of two regions corresponding to regions 2 and 4 of a group 1 factor, which are involved in the interaction with the Ϫ10 and Ϫ35 regions of the promoter, respectively. Bacterial genomic sequences suggest that many bacteria have multiple ECF factors (18).Thermus thermophilus HB8, which belongs to the phylum Deinococcus-Thermus, is an extremely thermophilic bacterium that was isolated from the water at a Japanese hot spring and can grow at 47 to 85°C, with an optimum temperature range of 65 to 72°C (20). The complete genomic sequence of this strain has been determined (NCBI accession numbers NC_006461, NC_006462, and NC_006463) and shows that the genome is composed of 1.85-megabase-pair chromosomal DNA, 0.26-megabase-pair plasmid pTT27, and 9.32-kilobase-pair plasmid pTT8, encoding 1,973, 251, and 14 open reading frames (ORFs), respectively. T. thermophilus HB8 has a typical bacterium-type RNAP, with the housekeeping A (29, 32). In addition to A

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Section: With the Combination Of In Vitro Transcription Assay And Genmentioning

confidence: 99%

Identification of Promoters Recognized by RNA Polymerase-σ ^E Holoenzyme from Thermus thermophilus HB8

et al. 2007

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“…The selenomethionine (SeMet) substituted protein was synthesized by a cell‐free system, as described (Kigawa et al 2002; Wada et al 2003), and purified in the same way as the native protein.…”

Section: Methodsmentioning

confidence: 99%

Crystal structure of a novel polyisoprenoid‐binding protein from Thermus thermophilus HB8

et al. 2005

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The isoprenoid quinones exist widely among prokaryotes and eukaryotes. They play essential roles in respiratory electron transport and in controlling oxidative stress and gene regulation. In the isoprenoid quinone biosynthetic pathway, polyprenyl pyrophosphates are used as isoprenoid side-chain precursors. Here we report the crystal structure of a novel polyprenyl pyrophosphate binding protein, TT1927b, from Thermus thermophilus HB8, complexed with its ligand. This protein belongs to the YceI-like family in the Pfam database, and its sequence homologs are present in a broad range of bacteria and archaea. The structure consists of an extended, eight-stranded, antiparallel ␤-barrel. In the hydrophobic pore of the barrel, the protein binds the polyisoprenoid chain by hydrophobic interactions. Its overall structure resembles the lipocalin fold, but there is no sequence homology between TT1927b and the lipocalin family of proteins.

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“…The SeMet substituted protein was synthesized by the Escherichia coli cell-free system. [43][44][45][46] The reaction solution was centrifuged at 16,000g at 4°C for 20 min. The cell lysate was loaded onto a HisTrap (GE Healthcare Bio-Sciences) column (5 ml), previously equilibrated with 20 mM Tris-HCl buffer (pH 8.0) containing 1 M NaCl and 15 mM imidazole, and was eluted with 20 mM Tris-HCl buffer (pH 8.0) containing 500 mM NaCl and 500 mM imidazole.…”

Section: Protein Preparation and Crystallizationmentioning

confidence: 99%

The Crystal Structure of Mouse Nup35 Reveals Atypical RNP Motifs and Novel Homodimerization of the RRM Domain

Handa

Kukimoto-Niino

Akasaka

et al. 2006

Journal of Molecular Biology

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Structure of a conserved CoA-binding protein synthesized by a cell-free system

Cited by 18 publications

References 20 publications

Identification of Promoters Recognized by RNA Polymerase-σ ^E Holoenzyme from Thermus thermophilus HB8

Identification of Promoters Recognized by RNA Polymerase-σ ^E Holoenzyme from Thermus thermophilus HB8

Crystal structure of a novel polyisoprenoid‐binding protein from Thermus thermophilus HB8

The Crystal Structure of Mouse Nup35 Reveals Atypical RNP Motifs and Novel Homodimerization of the RRM Domain

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Structure of a conserved CoA-binding protein synthesized by a cell-free system

Cited by 18 publications

References 20 publications

Identification of Promoters Recognized by RNA Polymerase-σ E Holoenzyme from Thermus thermophilus HB8

Identification of Promoters Recognized by RNA Polymerase-σ E Holoenzyme from Thermus thermophilus HB8

Crystal structure of a novel polyisoprenoid‐binding protein from Thermus thermophilus HB8

The Crystal Structure of Mouse Nup35 Reveals Atypical RNP Motifs and Novel Homodimerization of the RRM Domain

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Identification of Promoters Recognized by RNA Polymerase-σ ^E Holoenzyme from Thermus thermophilus HB8

Identification of Promoters Recognized by RNA Polymerase-σ ^E Holoenzyme from Thermus thermophilus HB8