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- PDB-7oy2: High resolution structure of cytochrome bd-II oxidase from E. coli -

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Basic information

Entry
Database: PDB / ID: 7oy2
TitleHigh resolution structure of cytochrome bd-II oxidase from E. coli
Components
  • (Cytochrome bd-II ubiquinol oxidase subunit ...) x 2
  • Putative cytochrome bd-II ubiquinol oxidase subunit AppX
KeywordsOXIDOREDUCTASE / Terminal oxidase High resolution Membrane protein Membrane enzyme Oxygen reductase bd oxidase
Function / homology
Function and homology information


ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / cytochrome complex / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cell outer membrane / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Membrane bound YbgT-like / Membrane bound YbgT-like protein / 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 / Chem-DK8 / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME B/C / OXYGEN MOLECULE / Chem-POV / Putative cytochrome bd-II ubiquinol oxidase subunit AppX / Cytochrome bd-II ubiquinol oxidase subunit 2 / Cytochrome bd-II ubiquinol oxidase subunit 1
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.06 Å
AuthorsGrund, T.N. / Wu, D. / Bald, D. / Michel, H. / Safarian, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck SocietyNobel laureate fellowship Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Mechanistic and structural diversity between cytochrome isoforms of .
Authors: Tamara N Grund / Melanie Radloff / Di Wu / Hojjat G Goojani / Luca F Witte / Wiebke Jösting / Sabine Buschmann / Hannelore Müller / Isam Elamri / Sonja Welsch / Harald Schwalbe / Hartmut ...Authors: Tamara N Grund / Melanie Radloff / Di Wu / Hojjat G Goojani / Luca F Witte / Wiebke Jösting / Sabine Buschmann / Hannelore Müller / Isam Elamri / Sonja Welsch / Harald Schwalbe / Hartmut Michel / Dirk Bald / Schara Safarian /
Abstract: The treatment of infectious diseases caused by multidrug-resistant pathogens is a major clinical challenge of the 21st century. The membrane-embedded respiratory cytochrome -type oxygen reductase is ...The treatment of infectious diseases caused by multidrug-resistant pathogens is a major clinical challenge of the 21st century. The membrane-embedded respiratory cytochrome -type oxygen reductase is a critical survival factor utilized by pathogenic bacteria during infection, proliferation and the transition from acute to chronic states. encodes for two cytochrome isoforms that are both involved in respiration under oxygen limited conditions. Mechanistic and structural differences between () and () operon encoded cytochrome variants have remained elusive in the past. Here, we demonstrate that cytochrome - catalyzes oxidation of benzoquinols while possessing additional specificity for naphthoquinones. Our data show that although menaquinol-1 (MK1) is not able to directly transfer electrons onto cytochrome from , it has a stimulatory effect on its oxygen reduction rate in the presence of ubiquinol-1. We further determined cryo-EM structures of cytochrome - to high resolution of 2.1 Å. Our structural insights confirm that the general architecture and substrate accessible pathways are conserved between the two oxidase isoforms, but two notable differences are apparent upon inspection: (i) does not contain a CydH-like subunit, thereby exposing heme to the membrane environment and (ii) the AppB subunit harbors a structural demethylmenaquinone-8 molecule instead of ubiquinone-8 as found in CydB of Our work completes the structural landscape of terminal respiratory oxygen reductases of and suggests that structural and functional properties of the respective oxidases are linked to quinol-pool dependent metabolic adaptations in .
History
DepositionJun 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code

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Structure visualization

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Assembly

Deposited unit
B: Cytochrome bd-II ubiquinol oxidase subunit 2
C: Cytochrome bd-II ubiquinol oxidase subunit 1
X: Putative cytochrome bd-II ubiquinol oxidase subunit AppX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,36410
Polymers106,8473
Non-polymers4,5167
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Cytochrome bd-II ubiquinol oxidase subunit ... , 2 types, 2 molecules BC

#1: Protein Cytochrome bd-II ubiquinol oxidase subunit 2 / Cytochrome bd-II oxidase subunit II


Mass: 42448.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: appB, cbdB, cyxB, b0979, JW0961 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): CLY
References: UniProt: P26458, ubiquinol oxidase (H+-transporting)
#2: Protein Cytochrome bd-II ubiquinol oxidase subunit 1 / Cytochrome bd-II oxidase subunit I


Mass: 57962.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: appC, cbdA, cyxA, b0978, JW0960 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): CLY
References: UniProt: P26459, ubiquinol oxidase (H+-transporting)

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Protein , 1 types, 1 molecules X

#3: Protein Putative cytochrome bd-II ubiquinol oxidase subunit AppX


Mass: 6436.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: appX, yccB, b4592, JW0961.1, b0979.1 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): CLY / References: UniProt: P24244

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Non-polymers , 7 types, 31 molecules

#4: Chemical ChemComp-CDN / CARDIOLIPIN


Mass: 1151.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C58H120O17P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DK8 / 2-[(2~{E},6~{E},10~{Z},14~{E},18~{E},22~{E},26~{E})-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaenyl]naphthalene-1,4-dione / demethlymenaquinone-8


Mass: 703.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H70O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#7: 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 / Feature type: SUBJECT OF INVESTIGATION
#8: 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
#9: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 from E. coli composed of subunit AppB, AppC and AppX
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.104 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Source (recombinant)Organism: Escherichia coli (strain K12) (bacteria)
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris1
2100 mMNaCl1
30.002 % (w/v)LMNG1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 108 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
4Gctf1.06CTF correction
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 533309 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0057326
ELECTRON MICROSCOPYf_angle_d0.8910002
ELECTRON MICROSCOPYf_dihedral_angle_d27.151049
ELECTRON MICROSCOPYf_chiral_restr0.0431087
ELECTRON MICROSCOPYf_plane_restr0.0061183

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