2O5J: Crystal Structure Of The T. Thermophilus Rnap Polymerase Elongation Complex With The Ntp Substrate Analog

Citation:
Abstract
The mechanism of substrate loading in multisubunit RNA polymerase is crucial for understanding the general principles of transcription yet remains hotly debated. Here we report the 3.0-A resolution structures of the Thermus thermophilus elongation complex (EC) with a non-hydrolysable substrate analogue, adenosine-5'-[(alpha,beta)-methyleno]-triphosphate (AMPcPP), and with AMPcPP plus the inhibitor streptolydigin. In the EC/AMPcPP structure, the substrate binds to the active ('insertion') site closed through refolding of the trigger loop (TL) into two alpha-helices. In contrast, the EC/AMPcPP/streptolydigin structure reveals an inactive ('preinsertion') substrate configuration stabilized by streptolydigin-induced displacement of the TL. Our structural and biochemical data suggest that refolding of the TL is vital for catalysis and have three main implications. First, despite differences in the details, the two-step preinsertion/insertion mechanism of substrate loading may be universal for all RNA polymerases. Second, freezing of the preinsertion state is an attractive target for the design of novel antibiotics. Last, the TL emerges as a prominent target whose refolding can be modulated by regulatory factors.
PDB ID: 2O5JDownload
MMDB ID: 104937
PDB Deposition Date: 2006/12/6
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 3  Å
Source Organism:
Thermus thermophilus HB8
Similar Structures:
Biological Unit for 2O5J: octameric; determined by author
Molecular Components in 2O5J
Label Count Molecule
Proteins (5 molecules)
2
DNA-directed RNA Polymerase Alpha Chain(Gene symbol: TTHA1664)
Molecule annotation
1
DNA-directed RNA Polymerase Beta Chain(Gene symbol: rpoB)
Molecule annotation
1
DNA-directed RNA Polymerase Beta' Chain(Gene symbol: TTHA1812)
Molecule annotation
1
DNA-directed RNA Polymerase Omega Chain(Gene symbol: rpoZ)
Molecule annotation
Nucleotides(3 molecules)
1
5'-d(p*cp*cp*cp*tp*gp*tp*cp*tp*gp*gp*cp*gp*tp*tp*cp*gp*cp*g P*cp*gp*cp*cp*g)-3'
Molecule annotation
1
5'-r(p*gp*ap*gp*up*cp*up*gp*cp*gp*gp*cp*gp*cp*gp*cp*g)-3'
Molecule annotation
1
5'-d(*ap*ap*cp*gp*cp*cp*ap*gp*ap*cp*ap*gp*gp*g)-3'
Molecule annotation
Chemicals (5 molecules)
1
2
2
2
3
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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