4XSX

Crystal structure of CBR 703 bound to Escherichia coli RNA polymerase holoenzyme

Summary for 4XSX

• Entry DOI: 10.2210/pdb4xsx/pdb
• Related: 4XSY 4XSZ
• Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... (8 entities in total)
• Functional Keywords: bacterial rna polymerase antibiotic complex, transcription-antibiotic complex, transcription/antibiotic
• Biological source: Escherichia coli (strain K12); More
• Cellular location: Cytoplasm : P00579
• Total number of polymer chains: 12
• Total formula weight: 860212.15

Authors

Bae, B.,Darst, S.A. (deposition date: 2015-01-22, release date: 2015-07-22, Last modification date: 2023-09-27)

Primary citation

Bae, B.,Nayak, D.,Ray, A.,Mustaev, A.,Landick, R.,Darst, S.A.
CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition.
Proc.Natl.Acad.Sci.USA, 112:E4178-E4187, 2015

PubMed Abstract: RNA polymerase inhibitors like the CBR class that target the enzyme's complex catalytic center are attractive leads for new antimicrobials. Catalysis by RNA polymerase involves multiple rearrangements of bridge helix, trigger loop, and active-center side chains that isomerize the triphosphate of bound NTP and two Mg(2+) ions from a preinsertion state to a reactive configuration. CBR inhibitors target a crevice between the N-terminal portion of the bridge helix and a surrounding cap region within which the bridge helix is thought to rearrange during the nucleotide addition cycle. We report crystal structures of CBR inhibitor/Escherichia coli RNA polymerase complexes as well as biochemical tests that establish two distinct effects of the inhibitors on the RNA polymerase catalytic site. One effect involves inhibition of trigger-loop folding via the F loop in the cap, which affects both nucleotide addition and hydrolysis of 3'-terminal dinucleotides in certain backtracked complexes. The second effect is trigger-loop independent, affects only nucleotide addition and pyrophosphorolysis, and may involve inhibition of bridge-helix movements that facilitate reactive triphosphate alignment.

PubMed: 26195788
DOI: 10.1073/pnas.1502368112

Experimental method

X-RAY DIFFRACTION (3.708 Å)