7U22 | pdb_00007u22

Mycobacterium tuberculosis RNA polymerase sigma A holoenzyme open promoter complex containing UMN-7

PDB DOI: https://doi.org/10.2210/pdb7U22/pdb
NAKB: 7U22

Classification: ANTIBIOTIC
Organism(s): Mycobacterium tuberculosis
Expression System: Mycobacterium tuberculosis
Mutation(s): No

Deposited: 2022-02-22 Released: 2022-10-19
Deposition Author(s): Molodtsov, V., Ebright, R.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.87 Å
R-Value Free:
0.278 (Depositor), 0.273 (DCC)
R-Value Work:
0.240 (Depositor), 0.239 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Redesign of Rifamycin Antibiotics to Overcome ADP-Ribosylation-Mediated Resistance.

Lan, T., Ganapathy, U.S., Sharma, S., Ahn, Y.M., Zimmerman, M., Molodtsov, V., Hegde, P., Gengenbacher, M., Ebright, R.H., Dartois, V., Freundlich, J.S., Dick, T., Aldrich, C.C.

(2022) Angew Chem Int Ed Engl 61: e202211498-e202211498

PubMed: 36222275 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.202211498
Primary Citation Related Structures:
7U22

PubMed Abstract:
Rifamycin antibiotics are a valuable class of antimicrobials for treating infections by mycobacteria and other persistent bacteria owing to their potent bactericidal activity against replicating and non-replicating pathogens. However, the clinical utility of rifamycins against Mycobacterium abscessus is seriously compromised by a novel resistance mechanism, namely, rifamycin inactivation by ADP-ribosylation. Using a structure-based approach, we rationally redesign rifamycins through strategic modification of the ansa-chain to block ADP-ribosylation while preserving on-target activity. Validated by a combination of biochemical, structural, and microbiological studies, the most potent analogs overcome ADP-ribosylation, restored their intrinsic low nanomolar activity and demonstrated significant in vivo antibacterial efficacy. Further optimization by tuning drug disposition properties afforded a preclinical candidate with remarkable potency and an outstanding pharmacokinetic profile.

Organizational Affiliation

Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 308 SE Harvard St SE, Minneapolis, MN 55455, USA.

Macromolecule Content

Total Structure Weight: 435.38 kDa
Atom Count: 25,925
Modeled Residue Count: 3,275
Deposited Residue Count: 3,865
Unique protein chains: 5
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A, B	347	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: rpoA EC: 2.7.7.6
UniProt
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGZ1 Go to UniProtKB: P9WGZ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGZ1
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	C	1,178	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: rpoB EC: 2.7.7.6
UniProt
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGY9 Go to UniProtKB: P9WGY9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGY9
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D	1,316	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: rpoC, rpoC_1, rpoC_2, DKC2_0716, ERS007665_00591, ERS023446_00410, ERS031537_00289, ERS124361_01694, EUB02_01475, EUB03_00860... rpoC, rpoC_1, rpoC_2, DKC2_0716, ERS007665_00591, ERS023446_00410, ERS031537_00289, ERS124361_01694, EUB02_01475, EUB03_00860, EUB11_05575, SAMEA2682835_07420, SAMEA2682864_01702 EC: 2.7.7.6
UniProt
Find proteins for P9WGY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGY7 Go to UniProtKB: P9WGY7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGY7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	E	110	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: rpoZ, DKC2_1480, DSI35_24025, ERS007657_03145, ERS007661_02963, ERS007663_02972, ERS007665_03743, ERS007670_03615, ERS007679_02942, ERS007681_04445... rpoZ, DKC2_1480, DSI35_24025, ERS007657_03145, ERS007661_02963, ERS007663_02972, ERS007665_03743, ERS007670_03615, ERS007679_02942, ERS007681_04445, ERS007722_03066, ERS007741_03196, ERS023446_03677, ERS024213_01369, ERS024276_01577, ERS027644_00478, ERS027646_01439, ERS027651_03169, ERS027653_00843, ERS027659_01429, ERS027661_02200, ERS027666_04715, ERS031537_03443, EU767_08910, EU768_15085, EU769_05250, EU770_14555, EU771_05130, EU773_14340, EU774_06465, EU775_07590, EU776_17830, EU777_06800, EUB02_12495, EUB03_09550, EUB06_03645, EUB07_12165, EUB08_05285, EUB09_00425, EUB10_04215, EUB11_10790, EUB13_01060, EUB14_01055, EUB16_00425, SAMEA2682864_01599, SAMEA2683035_01133 EC: 2.7.7.6
UniProt
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGY5 Go to UniProtKB: P9WGY5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGY5
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor SigA	F	528	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: sigA, hrdB_2, E5M05_04395, E5M52_03770, ERS007663_03246, ERS007679_00877, ERS007720_03380, ERS007722_02638, ERS013440_01579, ERS024276_00878... sigA, hrdB_2, E5M05_04395, E5M52_03770, ERS007663_03246, ERS007679_00877, ERS007720_03380, ERS007722_02638, ERS013440_01579, ERS024276_00878, ERS027646_01351, ERS027661_00252, FPJ30_14815, FPJ31_14925, FPJ32_14805, FPJ33_14840, FPJ34_14810, FPJ35_14895, FPJ36_14815, FPJ37_14795, FPJ38_14835, FPJ39_14805, FPJ40_14780, FPJ41_14820, FPJ42_14710, FPJ43_14795, FPJ44_14890, FPJ45_14810, FPJ46_14810, FPJ47_14805, FPJ48_14815, FPJ49_14795, FPJ50_14780, FPJ51_14775, FPJ52_14815, FPJ53_14810, FPJ54_14810, FPJ55_14940, FPJ56_14795, FPJ57_14805, FPJ58_14795, FPJ59_14815, FPJ60_14800, FPJ61_14810, FPJ62_14770, FPJ63_14840, FPJ64_14895, FPJ65_14800, FPJ66_14800, FPJ67_14845, FPJ69_14845, FPJ70_14845, FPJ71_14840, FPJ72_13570, FPJ73_14770, FPJ76_14775, FPJ77_14810, FPJ78_14815, FPJ79_14755, FPJ80_14870, FPJ81_14945, FPJ82_15000, FPJ83_06790, FPJ84_14750, FPJ85_06790, FPJ86_06790, FPJ87_06790, FPJ88_14760, FPJ89_14830, FPJ90_14780, FPJ91_14825, FPJ92_14790, FPJ93_14765, FPJ94_13565, FPJ95_14765, FPJ96_14935, FPJ97_14820, FPJ98_14805, FPJ99_14805, FPK00_14720, FPK01_14735, FPK02_14730, FPK03_14735, FPK04_14750, FPK05_14830, FPK06_14715, FPK07_14740, FPK08_14915, FPK09_14905, FPK10_13550, FPK11_14770, FPK12_14740, FPK13_14815, FPK14_14750, FPK16_14740, FPK17_14835, FPK18_14780, FPK19_14825, FPK20_14820, FPK21_14790, FPK22_14780, HRD52_14230, HRD53_14220, SAMEA2683035_01696
UniProt
Find proteins for P9WGI1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGI1 Go to UniProtKB: P9WGI1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGI1
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 6
T DNA	G	16	Mycobacterium tuberculosis
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 7
NT DNA	H	23	Mycobacterium tuberculosis
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KYO (Subject of Investigation/LOI) Query on KYO Download:Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	(9S,14S,15R,16S,17R,18R,19R,20S,21S,25R)-5,6,18,20-tetrahydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-(2-methylpropyl)-10,26-dioxo-1,3,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl benzoate C₅₁ H₇₂ N₄ O₁₁ MCRVPMWRSBLOPF-ZGLABKAESA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D]	J [auth D], K [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain J [auth D] Focus chain K [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]