6C7S | pdb_00006c7s

Structure of Rifampicin Monooxygenase with Product Bound

PDB DOI: https://doi.org/10.2210/pdb6C7S/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nocardia farcinica IFM 10152
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-01-23 Released: 2018-04-18
Deposition Author(s): Liu, L.-K., Tanner, J.J.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.241 (Depositor), 0.242 (DCC)
R-Value Work:
0.200 (Depositor), 0.201 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural Evidence for Rifampicin Monooxygenase Inactivating Rifampicin by Cleaving Its Ansa-Bridge.

Liu, L.K., Dai, Y., Abdelwahab, H., Sobrado, P., Tanner, J.J.

(2018) Biochemistry 57: 2065-2068

PubMed: 29578336 Search on PubMed
DOI: https://doi.org/10.1021/acs.biochem.8b00190
Primary Citation Related Structures:
6C7S

PubMed Abstract:
Rifampicin monooxygenase (RIFMO) decreases the potency of rifampicin (RIF) by converting it to oxidative products. Further decomposition of RIF has been observed in bacteria producing RIFMO and contributes to RIFMO-mediated drug resistance. Here we report the first crystal structure of RIFMO in complex with the hydroxylated RIF product. The 2.10 Å resolution structure reveals a breach of the ansa aliphatic chain of RIF between naphthoquinone C2 and amide N1. Our data suggest that RIFMO catalyzes the hydroxylation of RIF at the C2 atom followed by cleavage of the ansa linkage, which leads to inactivation of the antibiotic by preventing key contacts with the RNA polymerase target.

Organizational Affiliation

Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24061 , United States.

Macromolecule Content

Total Structure Weight: 53.69 kDa
Atom Count: 4,084
Modeled Residue Count: 473
Deposited Residue Count: 476
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative rifampin monooxygenase	A	476	Nocardia farcinica IFM 10152	Mutation(s): 0 Gene Names: rox, NFA_35380 EC: 1.14.13.211
UniProt
Find proteins for Q5YTV5 (Nocardia farcinica (strain IFM 10152)) Explore Q5YTV5 Go to UniProtKB: Q5YTV5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5YTV5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RFH (Subject of Investigation/LOI) Query on RFH Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(1E,3S,4R,5S,6R,7R,8R,9S,10S,11E,13E)-15-amino-1-{[(2S)-5,7-dihydroxy-2,4-dimethyl-8-{(E)-[(4-methylpiperazin-1-yl)imino]methyl}-1,6,9-trioxo-1,2,6,9-tetrahydronaphtho[2,1-b]furan-2-yl]oxy}-7,9-dihydroxy-3-methoxy-4,6,8,10,14-pentamethyl-15-oxopentadeca-1,11,13-trien-5-yl acetate C₄₃ H₅₈ N₄ O₁₃ ABIUUBSHMGGSQA-ONSLPDPNSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.241 (Depositor), 0.242 (DCC)
R-Value Work: 0.200 (Depositor), 0.201 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.877	α = 90
b = 81.877	β = 90
c = 286.205	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-04-18

Deposition Author(s):

Liu, L.-K.

Tanner, J.J.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1506206
National Science Foundation (NSF, United States)	United States	MCB 1021384

Revision History (Full details and data files)

Version 1.0: 2018-04-18
Type: Initial release
Version 1.1: 2019-02-20
Changes: Author supporting evidence, Data collection, Derived calculations, Structure summary
Version 1.2: 2019-11-27
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description