8QH4

Crystal structure of reduced respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to oxidized 3-acetylpyridine adenine dinucleotide

PDB DOI: https://doi.org/10.2210/pdb8QH4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aquifex aeolicus VF5
Expression System: Escherichia coli B
Mutation(s): No

Deposited: 2023-09-06 Released: 2024-04-03
Deposition Author(s): Wohlwend, D., Friedrich, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.224
R-Value Work: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structures of 3-acetylpyridine adenine dinucleotide and ADP-ribose bound to the electron input module of respiratory complex I.

Wohlwend, D., Merono, L., Bucka, S., Ritter, K., Jessen, H.J., Friedrich, T.

(2024) Structure

PubMed: 38503292 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2024.02.013
Primary Citation of Related Structures:
8QG1, 8QGW, 8QH4, 8QH7, 8QHK

PubMed Abstract:
Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is a major enzyme of energy metabolism that couples NADH oxidation and ubiquinone reduction with proton translocation. The NADH oxidation site features different enzymatic activities with various nucleotides. While the kinetics of these reactions are well described, only binding of NAD ⁺ and NADH have been structurally characterized. Here, we report the structures of the electron input module of Aquifex aeolicus complex I with bound ADP-ribose and 3-acetylpyridine adenine dinucleotides at resolutions better than 2.0 Å. ADP-ribose acts as inhibitor by blocking the "ADP-handle" motif essential for nucleotide binding. The pyridine group of APADH is minimally offset from flavin, which could contribute to its poorer suitability as substrate. A comparison with other nucleotide co-structures surprisingly shows that the adenine ribose and the pyrophosphate moiety contribute most to nucleotide binding, thus all adenine dinucleotides share core binding modes to the unique Rossmann-fold in complex I.

Organizational Affiliation

Institute of Biochemistry, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.

Macromolecule Content

Total Structure Weight: 138.57 kDa
Atom Count: 10,209
Modelled Residue Count: 1,146
Deposited Residue Count: 1,188
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit E	A, C	160	Aquifex aeolicus VF5	Mutation(s): 0 Gene Names: nuoE, aq_574 EC: 7.1.1
UniProt
Find proteins for O66842 (Aquifex aeolicus (strain VF5)) Explore O66842 Go to UniProtKB: O66842
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O66842
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit F	B, D	434	Aquifex aeolicus VF5	Mutation(s): 0 Gene Names: nuoF
UniProt
Find proteins for O66841 (Aquifex aeolicus (strain VF5)) Explore O66841 Go to UniProtKB: O66841
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O66841
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A3D (Subject of Investigation/LOI) Query on A3D Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain X [auth D] MOL2 format, chain J [auth B] MOL2 format, chain X [auth D]	J [auth B], X [auth D]	3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE C₂₂ H₂₈ N₆ O₁₄ P₂ KPVQNXLUPNWQHM-RBEMOOQDSA-N		Interactions Focus chain J [auth B] Focus chain X [auth D] Interactions & Density Focus chain J [auth B] Focus chain X [auth D]
FNR (Subject of Investigation/LOI) Query on FNR Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain W [auth D] MOL2 format, chain I [auth B] MOL2 format, chain W [auth D]	I [auth B], W [auth D]	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL C₁₇ H₂₃ N₄ O₉ P YTNIXZGTHTVJBW-SCRDCRAPSA-N		Interactions Focus chain I [auth B] Focus chain W [auth D] Interactions & Density Focus chain I [auth B] Focus chain W [auth D]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain V [auth D] MOL2 format, chain H [auth B] MOL2 format, chain V [auth D]	H [auth B], V [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain V [auth D] Interactions & Density Focus chain H [auth B] Focus chain V [auth D]
FES (Subject of Investigation/LOI) Query on FES Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain R [auth C] MOL2 format, chain E [auth A] MOL2 format, chain R [auth C]	E [auth A], R [auth C]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain R [auth C] Interactions & Density Focus chain E [auth A] Focus chain R [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain L [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain Z [auth D]	AA [auth D] F [auth A] G [auth A] L [auth B] S [auth C] AA [auth D], F [auth A], G [auth A], L [auth B], S [auth C], T [auth C], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain Y [auth D] MOL2 format, chain K [auth B] MOL2 format, chain Y [auth D]	K [auth B], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain Y [auth D] Interactions & Density Focus chain K [auth B] Focus chain Y [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain DA [auth D] MOL2 format, chain DA [auth D]	DA [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Interactions & Density Focus chain DA [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain P [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain P [auth B]	BA [auth D] CA [auth D] M [auth B] N [auth B] O [auth B] BA [auth D], CA [auth D], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], U [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C]