PDBsum entry 6myt

Oxidoreductase/oxidoreductase inhibitor

PDB id: 6myt

Contents

Protein chains

611 a.a.

240 a.a.

139 a.a.

102 a.a.

Ligands

FAD

OAA

UNL ×59

PEG

FES

SF4

F3S

AT5

HEM

UMQ

3PE

Metals

__K

Waters ×202

References listed in PDB file

Key reference

Title

Crystallographic studies of the binding of ligands to ubiquinone site of mitochondrial respiratory complex

Authors

L.-S.Huang, E.A.Berry.

Ref.

TO BE PUBLISHED ...

PubMed id

34089891

Note: In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above have been manually determined.

Secondary reference #1

Title

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.

Authors

L.S.Huang, G.Sun, D.Cobessi, A.C.Wang, J.T.Shen, E.Y.Tung, V.E.Anderson, E.A.Berry.

Ref.

J Biol Chem, 2006, 281, 5965-5972. [DOI no: 10.1074/jbc.M511270200]

PubMed id

16371358

Figure 1.
FIGURE 1. Overall structure of mitochondrial complex II. The stereo ribbon diagram is colored yellow and brown (flavoprotein), green (iron protein), pink (large anchor polypeptide, chain C), and blue (small anchor peptide, chain D). The CAP domain of the flavoprotein is colored brown. The green space-filling model at the intersection between the CAP domain and the rest of the flavoprotein is the malate-like ligand, and the extended blue ball-and-stick model starting just to the right of that is the FAD cofactor. Note the first helix of anchor peptide (Chain C) packs against a helix of the IP.

Figure 4.
FIGURE 4. The dicarboxylate site in the 3-NP-treated enzyme. The density attributed to the ligand has shrunk and moved away from the flavin toward Arg^297 and His^253. It can be modeled by assuming two atoms from the backbone of 3-NP (C-3 and N) fuse with the guanidino group to form a five-membered ring, with loss of the two nitro oxygens. The carboxylate at the other end fits into the clearly forked density branching off the ring. 2F[o] - F[c] map contoured at 1.7 .

The above figures are reproduced from the cited reference which is an Open Access publication published by the ASBMB

Author's comment:  These structures confirmed the role of Arg297 in ligand binding (and presumably catalysis) at the dicarboxylate active site. This had been suspected from mutagenesis and from the structure of homologous Flavocytochrome c of Shewanella, but had never been shown before in Complex II superfamily.
Structure 1YQ4 confirms the covalent binding of the plant and fungal toxin 3-nitropropionate, showing that the catalytic base arginine A297 is covalently modified. This is in contrast to a previous model from the lower-resolution structure of porcine complex II with nitropropionate bound.
-Edward Berry

Secondary reference #2

Title

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.

Authors

L.S.Huang, J.T.Shen, A.C.Wang, E.A.Berry.

Ref.

Biochim Biophys Acta, 2006, 1757, 1073-1083. [DOI no: 10.1016/j.bbabio.2006.06.015]

PubMed id

16935256

Secondary reference #3

Title

Crystallization of mitochondrial respiratory complex ii from chicken heart: a membrane-Protein complex diffracting to 2.0 a.

Authors

L.S.Huang, T.M.Borders, J.T.Shen, C.J.Wang, E.A.Berry.

Ref.

Acta Crystallogr D Biol Crystallogr, 2005, 61, 380-387. [DOI no: 10.1107/S0907444905000181]

PubMed id

15805592

Figure 3.
Figure 3 Typical crystals of avian complex II. (a) and (b) show crystals in two different wells. (c) and (d) each show a crystal mounted in a nylon loop on the goniometer at beamline 5.0.2 at the ALS. See text for description.

Figure 4.
Figure 4 A diffraction pattern of orthorhombic chicken mitochondrial complex II: a 1.0° oscillation diffraction pattern from one of the better complex II crystals at ALS beamline 5.0.1, with exposure 120 s and distance 200 mm, recorded on the ADSC Quantum 210 detector. The entire detector surface (210 × 210 mm) is shown in the main picture. A circle is drawn at a resolution of 2.00 Å. A small square area around 2.0 Å in the upper right quadrant is shown with increased contrast and part of that area is enlarged 3× in the upper right inset. Another region in the low-resolution area is shown magnified 3× and with reduced contrast in the lower right inset. The crystal is mounted so that the c axis is about 45° from the spindle axis and rotated about the spindle axis until the c axis is nearly perpendicular to the beam for this exposure. The concentric lunes are made up of reflections with constant values of h, while k varies from upper left to lower right and l from lower left to upper right (diagonal lines of barely resolved spots).

The above figures are reproduced from the cited reference with permission from the IUCr

Secondary reference #4

Title

Crystal structure of mitochondrial respiratory membrane protein complex ii.

Authors

F.Sun, X.Huo, Y.Zhai, A.Wang, J.Xu, D.Su, M.Bartlam, Z.Rao.

Ref.

Cell, 2005, 121, 1043-1057. [DOI no: 10.1016/j.cell.2005.05.025]

PubMed id

15989954

Figure 1.
Figure 1. The Role of Complex II in the Mitochondrial Respiratory Chain

Figure 5.
Figure 5. Ubiquinone Binding Sites

The above figures are reproduced from the cited reference with permission from Cell Press