1. Investigation of the crystal structure of cytochrome ba 3 oxidase By Caroline Christian Based on the paper by Soulimane, T., et all “Structure and mechanism of the aberrant ba 3 -cytochrome c oxidase from Thermus thermophilus” EMBO Journal, 19 (1766-1776), 2000.

2. NADH Dehydro genase Succinate dehydrogenase bc 1 complex Cytochrome oxidase ATP synthase NADH NAD + e-e- Succinate Fumarate e-e- Quinol pool O 2 H 2 O e-e- e-e- cyt c e-e- e-e- e-e- e-e- H+H+ H+H+ H+H+ H+H+ ADP + P i ATP Respiratory chain Out In Complex I Complex II Complex III Complex IV

3. Three different types of heme-copper oxidases Out Type B - ba 3 oxidase Type C - cbb 3 oxidase Type A (mitochondrial aa 3 oxidase) = Copper atom = heme molecule (Iron atom)

4. Outside P side Inside N side Cytochrome ba 3 oxidase crystal structure 3 subunits- Subunit I, II and IIa Subunit I – 13 alpha helixes Subunit II – 1 alpha helix, 8 beta sheets Subunit IIa – 1 alpha helix

5. Critical residues needed for function of the heme-copper oxidases K and D channels X-ray crystal structure of type-A oxidase (Rhodobacter sphaeroides numbering)

6. Residues are the K channel residues posed in the paper Tyr 237* Ser 309 Thr 312* Tyr 244 Tyr 248* Ser 261* Glu 516 Asp 517 *= conservation Conservation in all 14 complete type B oxidases sequences

7. Residues are the D-channel residues posed in paper – Top view Three pores in the protein, two are blocked by each heme, one is blocked by D- channel.

8. Residues are the D-channel residues posed in paper – Side view Glu 17 Thr 21 Gln 82 Gln 86 Ser 109 Ser 153 Thr 156 Ser 197 Thr 231 Ile 235 No conservation

9. Critical residues needed for function of the heme-copper oxidases K and D channels X-ray crystal structure of type-A oxidase (Rhodobacter sphaeroides numbering)

10. Ile 235 replaces Glu 286 (R. sphaeroides type A) at the top of the D-channel? Ile 235

11. Ile 235 with all residues within 4 Angstroms of it

12. There are some other residues within 4 angstroms of Ile 235 that could be playing same role- Trp 193* Thr 231 Pro 234 Val 236* Phe 238* Trp 239* *= compete conservation