1smy | pdb_00001smy

File:1smy.gif

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1smy, resolution 2.70Å
Ligands:	ZN, MG and G4P
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Coordinates:	save as pdb, mmCIF, xml

Structural basis for transcription regulation by alarmone ppGpp

Overview

Guanosine-tetraphosphate (ppGpp) is a major regulator of stringent control, an adaptive response of bacteria to amino acid starvation. The 2.7 A resolution structure of the Thermus thermophilus RNA polymerase (RNAP) holoenzyme in complex with ppGpp reveals that ppGpp binds to the same site near the active center in both independent RNAP molecules in the crystal but in strikingly distinct orientations. Binding is symmetrical with respect to the two diphosphates of ppGpp and is relaxed with respect to the orientation of the nucleotide base. Different modes of ppGpp binding are coupled with asymmetry of the active site configurations. The results suggest that base pairing of ppGpp with cytosines in the nontemplate DNA strand might be an essential component of transcription control by ppGpp. We present experimental evidence highlighting the importance of base-specific contacts between ppGpp and specific cytosine residues during both transcription initiation and elongation.

About this Structure

1SMY is a Protein complex structure of sequences from Thermus thermophilus. Full crystallographic information is available from OCA.

Reference

Structural basis for transcription regulation by alarmone ppGpp., Artsimovitch I, Patlan V, Sekine S, Vassylyeva MN, Hosaka T, Ochi K, Yokoyama S, Vassylyev DG, Cell. 2004 Apr 30;117(3):299-310. PMID:15109491

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