8HCR

Cryo-EM structure of the Mycobacterium tuberculosis cytochrome bcc:aa3 supercomplex and a novel inhibitor targeting subunit cytochrome cI


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Aggregation State: PARTICLE 
  • Reconstruction Method: TOMOGRAPHY 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-Electron Microscopy Structure of the Mycobacterium tuberculosi s Cytochrome bcc : aa 3 Supercomplex and a Novel Inhibitor Targeting Subunit Cytochrome c I.

Mathiyazakan, V.Wong, C.F.Harikishore, A.Pethe, K.Gruber, G.

(2023) Antimicrob Agents Chemother 67: e0153122-e0153122

  • DOI: https://doi.org/10.1128/aac.01531-22
  • Primary Citation of Related Structures:  
    8HCR

  • PubMed Abstract: 

    The mycobacterial cytochrome bcc:aa 3 complex deserves the name "supercomplex" since it combines three cytochrome oxidases-cytochrome bc , cytochrome c , and cytochrome aa 3 -into one supramolecular machine and performs electron transfer for the reduction of oxygen to water and proton transport to generate the proton motive force for ATP synthesis. Thus, the bcc:aa 3 complex represents a valid drug target for Mycobacterium tuberculosis infections. The production and purification of an entire M. tuberculosis cytochrome bcc:aa 3 are fundamental for biochemical and structural characterization of this supercomplex, paving the way for new inhibitor targets and molecules. Here, we produced and purified the entire and active M. tuberculosis cyt- bcc:aa 3 oxidase, as demonstrated by the different heme spectra and an oxygen consumption assay. The resolved M. tuberculosis cyt- bcc:aa 3 cryo-electron microscopy structure reveals a dimer with its functional domains involved in electron, proton, oxygen transfer, and oxygen reduction. The structure shows the two cytochrome c I c II head domains of the dimer, the counterpart of the soluble mitochondrial cytochrome c , in a so-called "closed state," in which electrons are translocated from the bcc to the aa 3 domain. The structural and mechanistic insights provided the basis for a virtual screening campaign that identified a potent M. tuberculosis cyt- bcc:aa 3 inhibitor, cyt Mycc 1. cyt Mycc 1 targets the mycobacterium-specific α3-helix of cytochrome c I and interferes with oxygen consumption by interrupting electron translocation via the c I c II head. The successful identification of a new cyt- bcc:aa 3 inhibitor demonstrates the potential of a structure-mechanism-based approach for novel compound development.


  • Organizational Affiliation

    Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex Rieske iron-sulfur subunitA,
J [auth M]
429Mycobacterium tuberculosis variant bovis BCGMutation(s): 0 
Gene Names: 
Membrane Entity: Yes 
UniProt
Find proteins for P9WH23 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WH23
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome b subunitB,
K [auth N]
573Mycobacterium tuberculosis variant bovis BCGMutation(s): 0 
Gene Names: RN06_2696
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P9WP37 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WP37
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome c subunitC,
L [auth O]
280Mycobacterium tuberculosis variant bovis BCGMutation(s): 0 
Gene Names: qcrCRv2194MTCY190.05
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P9WP35 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME AA3 SUBUNIT CtaCD [auth E],
M [auth Q]
363Mycobacterium tuberculosis variant bovis BCGMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Probable cytochrome c oxidase subunit 1E [auth F],
N [auth R]
573Mycobacterium tuberculosis variant bovis BCGMutation(s): 0 
Gene Names: ctaDRv3043cMTV012.58c
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for P9WP71 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Probable cytochrome c oxidase subunit 3F [auth G],
O [auth S]
203Mycobacterium tuberculosis variant bovis BCGMutation(s): 0 
Gene Names: ctaERv2193MTCY190.04
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 4G [auth H],
P [auth T]
139Mycobacterium tuberculosis variant bovis BCGMutation(s): 0 
Gene Names: RN06_2699
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME AA3 SUBUNIT CtaJH [auth I],
Q [auth U]
79Mycobacterium tuberculosis variant bovis BCGMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupI6YDH3
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DUF5130 domain-containing proteinI [auth J],
R [auth V]
155Mycobacterium tuberculosis variant bovis BCGMutation(s): 0 
Gene Names: K60_025630
UniProt
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEA (Subject of Investigation/LOI)
Query on HEA

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EA [auth R],
FA [auth R],
X [auth F],
Y [auth F]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
HEC (Subject of Investigation/LOI)
Query on HEC

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CA [auth O],
DA [auth O],
V [auth C],
W [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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AA [auth N],
BA [auth N],
T [auth B],
U [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FES (Subject of Investigation/LOI)
Query on FES

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S [auth A],
Z [auth M]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Aggregation State: PARTICLE 
  • Reconstruction Method: TOMOGRAPHY 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Singapore)SingaporeNRF-CRP18-2017-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references
  • Version 1.2: 2023-06-28
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references