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- PDB-9r2g: Cytochrome bd II oxidase qOR-2 type from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 9r2g
TitleCytochrome bd II oxidase qOR-2 type from Mycobacterium smegmatis
Components
  • Cytochrome bd menaquinol oxidase subunit I
  • Cytochrome bd-I oxidase subunit II
KeywordsELECTRON TRANSPORT / MEMBRANE PROTEIN / ACTINOBACTERIA
Function / homology
Function and homology information


cytochrome complex / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / electron transfer activity / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome ubiquinol oxidase subunit 1 / Cytochrome ubiquinol oxidase subunit 2 / Cytochrome bd terminal oxidase subunit I / Cytochrome bd terminal oxidase subunit II
Similarity search - Domain/homology
CARDIOLIPIN / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME B/C / MENAQUINONE-9 / Cytochrome bd-I oxidase subunit II / Cytochrome bd menaquinol oxidase subunit I
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKovalova, T. / Janczak, M. / Adelroth, P. / Hogbom, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2019.0043 Sweden
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: The -II terminal oxidase employs a carboxylate shift mechanism.
Authors: Terezia Kovalova / Mateusz Janczak / Ana P Gamiz-Hernandez / Daniel Lundin / Soni Sharma / Johanna Vilhjálmsdóttir / Dan Sjöstrand / Ville R I Kaila / Martin Högbom / Pia Ädelroth /
Abstract: Cytochrome is a terminal oxidase expressed under low oxygen conditions and central for the survival of many pathogens. Here, we characterize the cyt -II from , a member of a hitherto uncharacterized ...Cytochrome is a terminal oxidase expressed under low oxygen conditions and central for the survival of many pathogens. Here, we characterize the cyt -II from , a member of a hitherto uncharacterized evolutionary group (qOR-2) of oxidases, by combining biochemical studies with cryo-electron microscopy (cryo-EM), and multiscale simulations. Overexpressing the operon in its native host led to production of a highly active -II ( = 30 e s) that together with a high-resolution (2.8 Å) cryo-EM structure and multiscale simulations reveal unique proton pathways and oxygen channels responsible for its function. We propose that a pH-dependent molecular switch, involving coordination changes of heme and surrounding bulky residues regulate substrate access into the active site. Taken together, our findings provide detailed mechanistic insight of qOR-2 type oxidases, and a basis for understanding the evolution of the superfamily.
History
DepositionApr 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome bd menaquinol oxidase subunit I
D: Cytochrome bd-I oxidase subunit II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1839
Polymers89,4942
Non-polymers5,6897
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein Cytochrome bd menaquinol oxidase subunit I


Mass: 50327.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: ythA, BIN_B_00771 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A653F9S4
#2: Protein Cytochrome bd-I oxidase subunit II


Mass: 39166.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: D806_054940 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A2U9PXA2

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Non-polymers , 5 types, 14 molecules

#3: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#4: Chemical ChemComp-HDD / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME


Mass: 632.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Chemical ChemComp-MQ9 / MENAQUINONE-9


Mass: 785.233 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C56H80O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cytochrome bd II oxidase / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 93.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200084 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 101.68 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00855944
ELECTRON MICROSCOPYf_angle_d0.78538147
ELECTRON MICROSCOPYf_chiral_restr0.0426889
ELECTRON MICROSCOPYf_plane_restr0.0042980
ELECTRON MICROSCOPYf_dihedral_angle_d16.2762075

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