1SMY

Structural basis for transcription regulation by alarmone ppGpp

Summary for 1SMY

• Entry DOI: 10.2210/pdb1smy/pdb
• Related: 1IW7
• Descriptor: DNA-directed RNA polymerase alpha chain, DNA-directed RNA polymerase beta chain, DNA-directed RNA polymerase beta' chain, ... (9 entities in total)
• Functional Keywords: rna polymerase holoenzyme, guanosine-tetraphosphate, ppgpp, transcription regulation, riken structural genomics/proteomics initiative, rsgi, structural genomics, transferase
• Biological source: Thermus thermophilus; More
• Total number of polymer chains: 12
• Total formula weight: 863537.34

Authors

Artsimovitch, I.,Patlan, V.,Sekine, S.,Vassylyeva, M.N.,Hosaka, T.,Ochi, K.,Yokoyama, S.,Vassylyev, D.G.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2004-03-10, release date: 2004-05-18, Last modification date: 2023-10-25)

Primary citation

Artsimovitch, I.,Patlan, V.,Sekine, S.,Vassylyeva, M.N.,Hosaka, T.,Ochi, K.,Yokoyama, S.,Vassylyev, D.G.
Structural basis for transcription regulation by alarmone ppGpp
Cell(Cambridge,Mass.), 117:299-310, 2004

PubMed Abstract: 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.

PubMed: 15109491
DOI: 10.1016/S0092-8674(04)00401-5

Experimental method

X-RAY DIFFRACTION (2.7 Å)