6DCF

Crystal structure of a Mycobacterium smegmatis transcription initiation complex with Rifampicin-resistant RNA polymerase and bound to kanglemycin A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.252 

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Literature

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

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

(2018) Nat Commun 9: 4147-4147

  • DOI: https://doi.org/10.1038/s41467-018-06587-2
  • Primary Citation of Related Structures:  
    6CCE, 6CCV, 6DCF

  • PubMed 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 ...

    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.

    Organizational Affiliation: 

    Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA. sbrady@rockefeller.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-binding protein RbpAA [auth J]114Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rbpA, MSMEG_3858, MSMEI_3768
UniProt
Find proteins for A0QZ11 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0QZ11
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaB [auth A],
C [auth B]		350Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoA, MSMEG_1524, MSMEI_1488
EC: 2.7.7.6
UniProt
Find proteins for A0QSL8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0QSL8
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaD [auth C]1,169Mycolicibacterium smegmatis MC2 155Mutation(s): 1 
Gene Names: rpoB, MSMEG_1367, MSMEI_1328
EC: 2.7.7.6
UniProt
Find proteins for P60281 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupP60281
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'E [auth D]1,317Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoC, MSMEG_1368, MSMEI_1329
EC: 2.7.7.6
UniProt
Find proteins for A0QS66 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaF [auth E]107Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoZ, MSMEG_3053, MSMEI_2977
EC: 2.7.7.6
UniProt
Find proteins for A0QWT1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigAG [auth F]466Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: sigA, MSMEG_2758
UniProt
Find proteins for A0QW02 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (31-MER)H [auth O]31synthetic construct
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (26-MER)I [auth P]26synthetic construct
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Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KNG
Query on KNG
Download Ideal Coordinates CCD File 
J [auth C]Kanglemycin A
C50 H67 N O19
RKRZBNCHQZDJPK-UAXKWEMASA-N		 Ligand Interaction
GLU
Query on GLU
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U [auth D]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N		 Ligand Interaction
SO4
Query on SO4
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K [auth C]
L [auth C]
M [auth C]
Q [auth D]
R [auth D]
K [auth C],
L [auth C],
M [auth C],
Q [auth D],
R [auth D],
S [auth D],
T [auth D],
V [auth F],
W [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
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N [auth D],
O [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
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X [auth F],
Y [auth F]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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P [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.252 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.25α = 90
b = 160.909β = 110.75
c = 136.864γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5 R01 GM114450

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence