PDBsum entry 4xsy

Transcription/antibiotic

PDB id: 4xsy

Contents

Protein chains

224 a.a.

1340 a.a.

1166 a.a.

89 a.a.

470 a.a.

1236 a.a.

79 a.a.

Ligands

42T ×2

Metals

_ZN ×4

_MG ×2

PDB id:

4xsy

Name:

Transcription/antibiotic

Title:

Crystal structure of cbr 9379 bound to escherichia coli RNA polymerase holoenzyme

Structure:

DNA-directed RNA polymerase subunit alpha. Chain: a, b, g, h. Synonym: rnap subunit alpha,RNA polymerase subunit alpha, transcriptase subunit alpha. DNA-directed RNA polymerase subunit beta. Chain: c, i. Synonym: rnap subunit beta,RNA polymerase subunit beta,transcriptase subunit beta. DNA-directed RNA polymerase subunit beta'.

Source:

Escherichia coli o139:h28 (strain e24377a / etec). Organism_taxid: 331111. Strain: e24377a / etec. Citrobacter koseri (strain atcc baa-895 / cdc 4225-83 / sgsc4696). Organism_taxid: 290338. Strain: atcc baa-895 / cdc 4225-83 / sgsc4696. Escherichia coli (strain k12).

Resolution:

4.01Å R-factor: 0.237 R-free: 0.270

Authors:

B.Bae,S.A.Darst

Key ref:

B.Bae et al. (2015). CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition. Proc Natl Acad Sci U S A, 112, E4178. PubMed id: 26195788 DOI: 10.1073/pnas.1502368112

Date:

22-Jan-15 Release date: 22-Jul-15

Protein chains

A7ZSI4  (RPOA_ECO24) -  DNA-directed RNA polymerase subunit alpha from Escherichia coli O139:H28 (strain E24377A / ETEC)

Seq: 329 a.a.

Struc: 224 a.a.

Protein chains

A7ZUK1  (RPOB_ECO24) -  DNA-directed RNA polymerase subunit beta from Escherichia coli O139:H28 (strain E24377A / ETEC)

Seq: 1342 a.a.

Struc: 1340 a.a.

Protein chain

A7ZUK2  (RPOC_ECO24) -  DNA-directed RNA polymerase subunit beta' from Escherichia coli O139:H28 (strain E24377A / ETEC)

Seq: 1407 a.a.

Struc: 1166 a.a.

Protein chain

A8ARN6  (RPOZ_CITK8) -  DNA-directed RNA polymerase subunit omega from Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)

Seq: 91 a.a.

Struc: 89 a.a.

Protein chains

P00579  (RPOD_ECOLI) -  RNA polymerase sigma factor RpoD from Escherichia coli (strain K12)

Seq: 613 a.a.

Struc: 470 a.a.

Protein chain

A7ZUK2  (RPOC_ECO24) -  DNA-directed RNA polymerase subunit beta' from Escherichia coli O139:H28 (strain E24377A / ETEC)

Seq: 1407 a.a.

Struc: 1236 a.a.

Protein chain

A8ARN6  (RPOZ_CITK8) -  DNA-directed RNA polymerase subunit omega from Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)

Seq: 91 a.a.

Struc: 79 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, G, H, I, J, K: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1073/pnas.1502368112

Proc Natl Acad Sci U S A 112:E4178 (2015)

PubMed id: 26195788

CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition.

B.Bae, D.Nayak, A.Ray, A.Mustaev, R.Landick, S.A.Darst.

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.