PDBsum entry 2e1c

Transcription/DNA

PDB id: 2e1c

Contents

Protein chain

147 a.a. *

DNA/RNA

Waters ×133

* Residue conservation analysis

PDB id:

2e1c

Name:

Transcription/DNA

Title:

Structure of putative hth-type transcriptional regulator ph1519/DNA complex

Structure:

DNA (5'- d( Dap Dgp Dtp Dgp Dap Dap Dap Dap Dtp Dtp Dtp Dtp Dtp Dcp Dap Dcp Da )-3'). Chain: b. Engineered: yes. DNA (5'- d( Dtp Dgp Dtp Dgp Dap Dap Dap Dap Dap Dtp Dtp Dtp Dtp Dcp Dap Dcp Dt )-3'). Chain: d.

Source:

Synthetic: yes. Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.10Å R-factor: 0.206 R-free: 0.230

Ensemble:

2 models

Authors:

H.Koike,M.Suzuki

Key ref:

K.Yokoyama et al. (2007). Feast/famine regulation by transcription factor FL11 for the survival of the hyperthermophilic archaeon Pyrococcus OT3. Structure, 15, 1542-1554. PubMed id: 18073105 DOI: 10.1016/j.str.2007.10.015

Date:

24-Oct-06 Release date: 04-Dec-07

Protein chain

O59188  (REG6_PYRHO) -  HTH-type transcriptional regulator FL11 from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 151 a.a.

Struc: 147 a.a.

DNA/RNA chains

A-G-T-G-A-A-A-A-T-T-T-T-T-C-A-C-A 17 bases

T-G-T-G-A-A-A-A-A-T-T-T-T-C-A-C-T 17 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.str.2007.10.015

Structure 15:1542-1554 (2007)

PubMed id: 18073105

Feast/famine regulation by transcription factor FL11 for the survival of the hyperthermophilic archaeon Pyrococcus OT3.

K.Yokoyama, S.A.Ishijima, H.Koike, C.Kurihara, A.Shimowasa, M.Kabasawa, T.Kawashima, M.Suzuki.

ABSTRACT

Transcriptional repressor FL11 from the hyperthermophilic archaeon, Pyrococcus OT3, was crystallized in its dimer form in complex with a DNA duplex, TGAAAWWWTTTCA. Chemical contacting of FL11 to the terminal 5 bps, and DNA bending by propeller twisting at WWW confirmed specificity of the interaction. Dimer-binding sites were identified in promoters of approximately 200 transcription units coding, for example, H+-ATPase and NAD(P)H dehydrogenase. In the presence of lysine, four FL11 dimers were shown to assemble into an octamer, thereby covering the fl11 promoter. In the "feast" mode, when P. OT3 grows on amino acids, the FL11 octamer will terminate transcription of fl11, as was shown in vitro, thereby derepressing transcription of many metabolic genes. In the "famine" mode in the absence of lysine, approximately 6000 FL11 dimers present per cell will arrest growth. This regulation resembles global regulation by Escherichia coli leucine-responsive regulatory protein, and hints at a prototype of transcription regulations now highly diverged.

Selected figure(s)

Figure 2.
Figure 2. Interaction of the FL11 Dimer and DNA in the Crystal Complex
(A) A ribbon diagram of the crystal complex. The DNA strand 5′-TG[T1G2A3A4A5]A6A7T8[T9T10T11C12A13]CT-3′ proceeds from left to right. The N termini of the two polypeptides are labeled. To T1G2A3A4A5/T5T4T3C2A1 and T9T10T11C12A13/T13G12A11A10A9 (crimson), a pair of Ala34-Thr37 (green) in FL11 form chemical contacts. The side chains of a pair of Arg25, His39, and Arg41 (black) form ionic interactions with DNA phosphates. Structures are represented using the Pymol program (DeLano and Lam, 2005).
(B) The FL11 dimer in the DNA complex (yellow) compared with that (green) crystallized with no DNA (PDB code, 1RI7) by best overlapping Cα atoms of Met67-Ile151 to an rmsd of 0.34 Å. The DNA in the crystal (cyan) is compared with a standard B-DNA (crimson) modeled with a server (Vlahovicek et al., 2003) by best overlaying the central three base pairs. Narrowing of the minor (m) groove and widening of the major (M) groove at the center of the crystallized DNA are indicated by arrows.
(C) Phosphate-phosphate distances over the major (M) and minor (m) grooves (upper), and propeller twists of base pairs (lower), measured using the 3DNA program (Lu and Olson, 2003). The major groove width of 16.6 Å and the minor groove width of 12.1 Å of the standard DNA (B) are indicated (upper).
(D) A view looking down the DNA double helix. The main chain of FL11 is colored green at Ala34-Thr37.
(E and F) Views looking into the DNA major groove from Ala34-Thr37, showing α helices 2 and 3 (F). (E) Yellow arrows indicate hydrogen bonds from donors to acceptors. Red broken lines indicate hydrophobic interactions. Water molecules 1 and 2 form hydrogen bonds to and from Glu35. (F) T methyl groups forming hydrophobic interactions with Leu24 or His39 are circled in red. Green broken lines indicate ionic interactions.
(G) A schematic representation of chemical contacts made to DNA from FL11. Black and white circles in DNA bases indicate hydrogen bond donors and acceptors, respectively. Gray circles indicate the methyl groups of T bases. Green lines indicate ionic interactions, and red lines hydrophobic contacts. Arrows indicate hydrogen bonds from donors to acceptors.
(H) The Ser36 side chain, whose geometry is fixed by a hydrogen bond from the main-chain NH of Thr37, donates a bifurcated hydrogen bond to N7 and O6 of guanine at basepair 2.
(I) The Arg41 side chain is in ionic interactions with the Asp6 and Asp9 side chains to contact a DNA phosphate group. Ionic interactions are indicated by green lines.

Figure 5.
Figure 5. In Vitro Transcription from Promoters
After in vitro transcription, mRNA was amplified by RT-PCR, and the synthesized DNAs were subjected to gel electrophoresis. When present, the lysine concentration was 5 mM and that of the FL11 dimer was 15, 50, 150, or 500 pmol/20 μl. Gels were stained with ethidium bromide and analyzed with an imager (BioRad, Pharos FX). Presented are one of two independent results obtained with fl11 (A), lysine synthesis (B), nad(p)h dehydrogenase (C), or h^+-atpase subunits I, K (D) promoter, and averages of relative intensities of bands measured in the two experiments (E–H).

The above figures are reprinted by permission from Cell Press: Structure (2007, 15, 1542-1554) copyright 2007.

Figures were selected by an automated process.