PDBsum entry 6dcf

Transcription/DNA/antibiotic

PDB id: 6dcf

Contents

Protein chains

85 a.a.

219 a.a.

858 a.a.

1176 a.a.

82 a.a.

297 a.a.

DNA/RNA

Ligands

KNG

SO4 ×9

GLU

EDO ×2

Metals

_ZN ×2

_MG

Waters ×7

PDB id:

6dcf

Name:

Transcription/DNA/antibiotic

Title:

Crystal structure of a mycobacterium smegmatis transcription initiation complex with rifampicin-resistant RNA polymerase and bound to kanglemycin a

Structure:

RNA polymerase-binding protein rbpa. Chain: j. Engineered: yes. DNA-directed RNA polymerase subunit alpha. Chain: a, b. Synonym: rnap subunit alpha,RNA polymerase subunit alpha, transcriptase subunit alpha. DNA-directed RNA polymerase subunit beta. Chain: c.

Source:

Mycobacterium smegmatis (strain atcc 700084 / mc(2)155). Organism_taxid: 246196. Strain: atcc 700084 / mc(2)155. Gene: rbpa, msmeg_3858, msmei_3768. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: rpob, msmeg_1367, msmei_1328. Expressed in: escherichia coli.

Resolution:

3.45Å R-factor: 0.252 R-free: 0.290

Authors:

M.Lilic,S.A.Darst,E.A.Campbell

Key ref:

J.Peek et al. (2018). Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism. Nat Commun, 9, 4147. PubMed id: 30297823 DOI: 10.1038/s41467-018-06587-2

Date:

06-May-18 Release date: 05-Sep-18

Protein chain

A0QZ11  (RBPA_MYCS2) -  RNA polymerase-binding protein RbpA from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)

Seq: 114 a.a.

Struc: 85 a.a.

Protein chains

A0QSL8  (RPOA_MYCS2) -  DNA-directed RNA polymerase subunit alpha from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)

Seq: 350 a.a.

Struc: 219 a.a.

Protein chain

P60281  (RPOB_MYCS2) -  DNA-directed RNA polymerase subunit beta from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)

Seq: 1169 a.a.

Struc: 858 a.a.*

Protein chain

A0QS66  (RPOC_MYCS2) -  DNA-directed RNA polymerase subunit beta' from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)

Seq: 1317 a.a.

Struc: 1176 a.a.

Protein chain

A0QWT1  (RPOZ_MYCS2) -  DNA-directed RNA polymerase subunit omega from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)

Seq: 107 a.a.

Struc: 82 a.a.

Protein chain

A0QW02  (A0QW02_MYCS2) -  RNA polymerase sigma factor SigA from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)

Seq: 466 a.a.

Struc: 297 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

G-C-T-T-G-A-C-A-A-A-A-G-T-G-T-T-A-A-A-T-T-G-T-G-C-T-A-T-A-C-T 31 bases

A-G-C-A-C-A-A-T-T-T-A-A-C-A-C-T-T-T-T-G-T-C-A-A-G-C 26 bases

Enzyme reactions

• Enzyme class: Chains A, B, D, E: 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: 10.1038/s41467-018-06587-2

Nat Commun 9:4147 (2018)

PubMed id: 30297823

Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism.

J.Peek, M.Lilic, D.Montiel, A.Milshteyn, I.Woodworth, J.B.Biggins, M.A.Ternei, P.Y.Calle, M.Danziger, T.Warrier, K.Saito, N.Braffman, A.Fay, M.S.Glickman, S.A.Darst, E.A.Campbell, S.F.Brady.

ABSTRACT

Rifamycin antibiotics (Rifs) target bacterial RNA polymerases (RNAPs) and are widely used to treat infections including tuberculosis. The utility of these compounds is threatened by the increasing incidence of resistance (Rif^R). As resistance mechanisms found in clinical settings may also occur in natural environments, here we postulated that bacteria could have evolved to produce rifamycin congeners active against clinically relevant resistance phenotypes. We survey soil metagenomes and identify a tailoring enzyme-rich family of gene clusters encoding biosynthesis of rifamycin congeners (kanglemycins, Kangs) with potent in vivo and in vitro activity against the most common clinically relevant Rif^R mutations. Our structural and mechanistic analyses reveal the basis for Kang inhibition of Rif^R RNAP. Unlike Rifs, Kangs function through a mechanism that includes interfering with 5'-initiating substrate binding. Our results suggest that examining soil microbiomes for new analogues of clinically used antibiotics may uncover metabolites capable of circumventing clinically important resistance mechanisms.