6MYS

Avian mitochondrial complex II with Atpenin A5 bound, sidechain outside

• PDB DOI:  https://doi.org/10.2210/pdb6MYS/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Gallus gallus
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2018-11-02 Released: 2019-11-06 
• Deposition Author(s): Berry, E.A., Huang, L.-S.
• Funding Organization(s): Department of Health & Human Services (HHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 0.237 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Literature

Crystallographic investigation of the ubiquinone binding site of respiratory Complex II and its inhibitors.

Huang, L.S., Lummen, P., Berry, E.A.

(2021) Biochim Biophys Acta Proteins Proteom 1869: 140679-140679

• PubMed: 34089891 
• DOI: https://doi.org/10.1016/j.bbapap.2021.140679
• Primary Citation of Related Structures:  
  6MYO, 6MYP, 6MYQ, 6MYR, 6MYS, 6MYT, 6MYU


• PubMed Abstract: 
  

The quinone binding site (Q-site) of Mitochondrial Complex II (succinate-ubiquinone oxidoreductase) is the target for a number of inhibitors useful for elucidating the mechanism of the enzyme. Some of these have been developed as fungicides or pesticides, and species-specific Q-site inhibitors may be useful against human pathogens. We report structures of chicken Complex II with six different Q-site inhibitors bound, at resolutions 2.0-2.4 Å. These structures show the common interactions between the inhibitors and their binding site. In every case a carbonyl or hydroxyl oxygen of the inhibitor is H-bonded to Tyr58 in subunit SdhD and Trp173 in subunit SdhB. Two of the inhibitors H-bond Ser39 in subunit SdhC directly, while two others do so via a water molecule. There is a distinct cavity that accepts the 2-substituent of the carboxylate ring in flutolanil and related inhibitors. A hydrophobic "tail pocket" opens to receive a side-chain of intermediate-length inhibitors. Shorter inhibitors fit entirely within the main binding cleft, while the long hydrophobic side chains of ferulenol and atpenin A5 protrude out of the cleft into the bulk lipid region, as presumably does that of ubiquinone. Comparison of mitochondrial and Escherichia coli Complex II shows a rotation of the membrane-anchor subunits by 7° relative to the iron‑sulfur protein. This rotation alters the geometry of the Q-site and the H-bonding pattern of SdhB:His216 and SdhD:Asp57. This conformational difference, rather than any active-site mutation, may be responsible for the different inhibitor sensitivity of the bacterial enzyme.

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Related Citations: 

• 3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme.
  Huang, L.S., Sun, G., Cobessi, D., Wang, A.C., Shen, J.T., Tung, E.Y., Anderson, V.E., Berry, E.A.
  (2006) J Biol Chem 281: 5965

• Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the "oxaloacetate-inhibited" state.
  Huang, L.S., Shen, J.T., Wang, A.C., Berry, E.A.
  (2006) Biochim Biophys Acta 1757: 1073

• Crystallization of mitochondrial respiratory complex II from chicken heart: a membrane-protein complex diffracting to 2.0 A.
  Huang, L.S., Borders, T.M., Shen, J.T., Wang, C.J., Berry, E.A.
  (2005) Acta Crystallogr D Biol Crystallogr 61: 380

• Crystal structure of mitochondrial respiratory membrane protein complex II.
  Sun, F., Huo, X., Zhai, Y., Wang, A., Xu, J., Su, D., Bartlam, M., Rao, Z.
  (2005) Cell 121: 1043

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Organizational Affiliation: 

Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 E. Adams Street, Syracuse, N.Y 13210, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 127.31 kDa 
• Atom Count: 9,014 
• Modelled Residue Count: 1,093 
• Deposited Residue Count: 1,116 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A	621	Gallus gallus	Mutation(s): 0  Gene Names: SDHA EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for Q9YHT1 (Gallus gallus) Explore Q9YHT1  Go to UniProtKB:  Q9YHT1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial	B	252	Gallus gallus	Mutation(s): 0  Gene Names: SDHB EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for Q9YHT2 (Gallus gallus) Explore Q9YHT2  Go to UniProtKB:  Q9YHT2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase cytochrome b, large subunit	C	140	Gallus gallus	Mutation(s): 0  Gene Names: SDHC EC: 1.3.5.1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial	D	103	Gallus gallus	Mutation(s): 0  Gene Names: SDHD, RCJMB04_23p7 Membrane Entity: Yes
UniProt
Find proteins for Q5ZIS0 (Gallus gallus) Explore Q5ZIS0  Go to UniProtKB:  Q5ZIS0

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
3PE	NA [auth D]	1,2-Distearoyl-sn-glycerophosphoethanolamine C41 H82 N O8 P LVNGJLRDBYCPGB-LDLOPFEMSA-N
HEM	FA [auth C]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
UMQ	GA [auth C]	UNDECYL-MALTOSIDE C23 H44 O11 UYEMNFYVTFDKRG-ZNGNCRBCSA-N
AT5	EA [auth C]	3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE C15 H21 Cl2 N O5 OVULNOOPECCZRG-CIUDSAMLSA-N
SF4	W [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
F3S	X [auth B]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-MZMDZPPWAW
FES	V [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
OAA	G [auth A]	OXALOACETATE ION C4 H3 O5 KHPXUQMNIQBQEV-UHFFFAOYSA-M
K	F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
UNL	AA [auth B], AB [auth D], BA [auth B], BB [auth D], CA [auth B], DA [auth B], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], O [auth A], OA [auth D], P [auth A], PA [auth D], Q [auth A], QA [auth D], R [auth A], RA [auth D], S [auth A], SA [auth D], T [auth A], TA [auth D], U [auth A], UA [auth D], VA [auth D], WA [auth D], XA [auth D], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	Unknown ligand NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ	C	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 0.237 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.68	α = 90
b = 84.424	β = 90
c = 293.019	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-06 
Deposition Author(s): Berry, E.A., Huang, L.-S.

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Funding Organization	Location	Grant Number
Department of Health & Human Services (HHS)	United States	1R01GM062563

Revision History  

• Version 1.0: 2019-11-06
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2021-07-07
  Changes: Database references, Derived calculations, Structure summary