PDBsum entry 1sig

Transcription regulation

PDB id: 1sig

Contents

Protein chain

305 a.a.

Waters ×333

References listed in PDB file

Key reference

Title

Crystal structure of a sigma 70 subunit fragment from e. Coli RNA polymerase.

Authors

A.Malhotra, E.Severinova, S.A.Darst.

Ref.

Cell, 1996, 87, 127-136. [DOI no: 10.1016/S0092-8674(00)81329-X]

PubMed id

8858155

Abstract

The 2.6 A crystal structure of a fragment of the sigma 70 promoter specificity subunit of E. coli RNA polymerase is described. Residues involved in core RNA polymerase binding lie on one face of the structure. On the opposite face, aligned along one helix, are exposed residues that interact with the -10 consensus promoter element (the Pribnow box), including four aromatic residues involved in promoter melting. The structure suggests one way in which DNA interactions may be inhibited in the absence of RNA polymerase and provides a framework for the interpretation of a large number of genetic and biochemical analyses.

Figure 4.
Figure 4. DNA Interaction Surface of σ^70[2](A) Stereo RIBBONS ([10]) diagram of the cluster of four helices comprising the conserved regions. The view is 180° about a vertical axis from the view of Figure 3. Helix 14, containing part of conserved region 2.3 and conserved region 2.4, runs nearly horizontally across the middle of the picture. Shown in yellow are residues that comprise the conserved hydrophobic core (Ile-119, Ile-123, Ala-375, Met-379, Val-380, Val-387, Ala-391, Leu-399, Leu-404, Leu-412, Ala-415, Val-416, Phe-419, Phe-427, Ala-431, Ile-435, Ile-439, Ile-443). Other residues are shown in color as follows: cyan, exposed conserved aromatic residues from region 2.3, important for promoter melting; orange, residues known to interact with the −12 position of the −10 consensus element; blue, conserved basic residues flanking the promoter recognition and promoter melting residues that may be involved in DNA phosphate backbone interactions.(B) Likely orientation of helix 14/nontemplate DNA strand interactions. The backbone of helix 14 is shown as a coil with the solvent-exposed face of the helix facing down. The α-carbon positions of residues important for promoter recognition or melting are indicated. Schematically illustrated below is the nontemplate strand sequence of the −10 consensus element. Interactions between specific residues and bases determined from genetic or biochemical studies are indicated by dashed lines. The interaction indicated between the residue at position 441 and the −13 position is not specific in the case of σ^70 (the −13 position is not conserved in the −10 element recognized by σ^70) but is indicated from genetic studies on alternative σ factors that recognize −10 elements with a conserved −13 position ([15]).

Figure 5.
Figure 5. Potential Autoinhibition of DNA BindingRIBBONS ([10]) diagram showing a view of the conserved region helices, vert, similar 90° about a vertical axis from the view of Figure 4. Helix 14 is viewed from the C-terminal end nearly down its axis. Selected conserved residues are color coded as follows: yellow, residues comprising conserved hydrophobic core; green, residues in region important for core RNAP binding; cyan, aromatic residues important for promoter melting; orange, residues important for recognition of the −12 position of the −10 consensus element. The location of core binding and DNA binding determinants on opposite sides of the structure is noted. Illustrated schematically are the sequence (in single-letter amino acid code) and charge of the 20-residue, disordered acidic loop (residues 192–211).

The above figures are reprinted by permission from Cell Press: Cell (1996, 87, 127-136) copyright 1996.

Secondary reference #1

Title

Domain organization of the escherichia coli RNA polymerase sigma 70 subunit.

Authors

E.Severinova, K.Severinov, D.Fenyö, M.Marr, E.N.Brody, J.W.Roberts, B.T.Chait, S.A.Darst.

Ref.

J Mol Biol, 1996, 263, 637-647. [DOI no: 10.1006/jmbi.1996.0604]

PubMed id

8947564

Figure 1.
Figure 1. Limited trypsinolysis of s 70 analyzed by SDS--PAGE on an 8% to 25% gradient PhastGel (Pharmacia). Reactions contained 60 pmol of s 70 and 0, 0.15, 0.19, 0.3, 0.4, 0.6, 1.2, or 3 pmol of trypsin (lanes 1 to 8, respectively).

Figure 5.
Figure 5. Competitive binding to core RNAP by s 70 2 and intact s 70 . Core RNAP (15 pmol in each reaction) was incubated with the indicated molar ratios of s 70 and s 70 2a and then analyzed by native PAGE on a 4% to 15% gradient PhastGel (Pharmacia).

The above figures are reproduced from the cited reference with permission from Elsevier