7DEG

Cryo-EM structure of a heme-copper terminal oxidase dimer provides insights into its catalytic mechanism

PDB DOI: https://doi.org/10.2210/pdb7DEG/pdb
EM Map EMD-30657: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Aquifex aeolicus VF5, Aquifex aeolicus
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2020-11-04 Released: 2021-08-04
Deposition Author(s): Fei, S., Hartmut, M., Yun, Z., Guoliang, Z., Shuangbo, Z.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

The Unusual Homodimer of a Heme-Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors.

Zhu, G., Zeng, H., Zhang, S., Juli, J., Tai, L., Zhang, D., Pang, X., Zhang, Y., Lam, S.M., Zhu, Y., Peng, G., Michel, H., Sun, F.

(2021) Angew Chem Int Ed Engl 60: 13323-13330

PubMed: 33665933 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/anie.202016785
Primary Citation of Related Structures:
7DEG

PubMed Abstract:
The heme-copper oxidase superfamily comprises cytochrome c and ubiquinol oxidases. These enzymes catalyze the transfer of electrons from different electron donors onto molecular oxygen. A B-family cytochrome c oxidase from the hyperthermophilic bacterium Aquifex aeolicus was discovered previously to be able to use both cytochrome c and naphthoquinol as electron donors. Its molecular mechanism as well as the evolutionary significance are yet unknown. Here we solved its 3.4 Å resolution electron cryo-microscopic structure and discovered a novel dimeric structure mediated by subunit I (CoxA2) that would be essential for naphthoquinol binding and oxidation. The unique structural features in both proton and oxygen pathways suggest an evolutionary adaptation of this oxidase to its hyperthermophilic environment. Our results add a new conceptual understanding of structural variation of cytochrome c oxidases in different species.

Organizational Affiliation

National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China.

Macromolecule Content

Total Structure Weight: 183.3 kDa
Atom Count: 12,852
Modelled Residue Count: 1,520
Deposited Residue Count: 1,532
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit I	A, D	587	Aquifex aeolicus VF5	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for O67937 (Aquifex aeolicus (strain VF5)) Explore O67937 Go to UniProtKB: O67937
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O67937
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome oxidase subunit IIa	B [auth C], E [auth F]	32	Aquifex aeolicus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for G0LWX8 (Aquifex aeolicus) Explore G0LWX8 Go to UniProtKB: G0LWX8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0LWX8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome oxidase subunit II	C [auth B], F [auth E]	147	Aquifex aeolicus	Mutation(s): 0
UniProt
Find proteins for G5DGC8 (Aquifex aeolicus) Explore G5DGC8 Go to UniProtKB: G5DGC8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G5DGC8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HAS Query on HAS Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth D]	G [auth A], Q [auth D]	HEME-AS C₅₄ H₆₄ Fe N₄ O₆ PDYODZVCODUKFH-ZOMLSHGTSA-L		Interactions Focus chain G [auth A] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain Q [auth D]
PGV Query on PGV Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain U [auth D] SDF format, chain W [auth F] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain U [auth D] MOL2 format, chain W [auth F]	K [auth A] M [auth A] N [auth C] P [auth D] U [auth D] K [auth A], M [auth A], N [auth C], P [auth D], U [auth D], W [auth F]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth C] Focus chain P [auth D] Focus chain U [auth D] Focus chain W [auth F] Interactions & Density Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth C] Focus chain P [auth D] Focus chain U [auth D] Focus chain W [auth F]
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain V [auth D] MOL2 format, chain L [auth A] MOL2 format, chain V [auth D]	L [auth A], V [auth D]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain L [auth A] Focus chain V [auth D] Interactions & Density Focus chain L [auth A] Focus chain V [auth D]
DLX Query on DLX Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain T [auth D] MOL2 format, chain J [auth A] MOL2 format, chain T [auth D]	J [auth A], T [auth D]	2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione C₄₅ H₆₆ O₂ HQTZEMLTZXAZEE-ZTUUOAHYSA-N		Interactions Focus chain J [auth A] Focus chain T [auth D] Interactions & Density Focus chain J [auth A] Focus chain T [auth D]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain R [auth D] MOL2 format, chain H [auth A] MOL2 format, chain R [auth D]	H [auth A], R [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain H [auth A] Focus chain R [auth D] Interactions & Density Focus chain H [auth A] Focus chain R [auth D]
CUA Query on CUA Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain X [auth E] MOL2 format, chain O [auth B] MOL2 format, chain X [auth E]	O [auth B], X [auth E]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain X [auth E] Interactions & Density Focus chain O [auth B] Focus chain X [auth E]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain S [auth D] MOL2 format, chain I [auth A] MOL2 format, chain S [auth D]	I [auth A], S [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain S [auth D] Interactions & Density Focus chain I [auth A] Focus chain S [auth D]