Investigation of the crystal structure of cytochrome ba 3 oxidase

Investigation of the crystal structure of cytochrome ba3 oxidase

By Caroline Christian

Based on the paper by Soulimane, T., et all “Structure and mechanism of the aberrant ba3-cytochrome c

oxidase from Thermus thermophilus” EMBO Journal, 19 (1766-1776), 2000.

NADHDehydrogenase

Succinate dehydrogenase

bc1 complex

Cytochrome oxidase

ATP synthase

NADHNAD+

e-

SuccinateFumarate

e-

Quinol pool

O2

H2O

e-

e-

cyt c

e-e-

e-

e-

H+H+ H+

H+

ADP + Pi ATP

Respiratory chain

Out

In

Complex I Complex II Complex III Complex IV

Three different types of heme-copper oxidases

Out

Type B - ba3 oxidase

Type C - cbb3 oxidase

Type A(mitochondrial

aa3 oxidase)

I I

c c cb b3a a3 b a3

In

II II III II I

= Copper atom

= heme molecule (Iron atom)

Outside P side

Inside N side

Cytochrome ba3 oxidase crystal structure3 subunits- Subunit I, II and IIa

Subunit I – 13 alpha helixes

Subunit II – 1 alpha helix, 8 beta sheets

Subunit IIa – 1 alpha helix

Critical residues needed for function of the heme-copper oxidasesK and D channels

X-ray crystal structure of type-A oxidase (Rhodobacter sphaeroides numbering)

Residues are the K channel residues posed in the paper

Tyr 237*Ser 309Thr 312*Tyr 244Tyr 248*Ser 261*Glu 516Asp 517*= conservation

Conservation in all 14 complete type B oxidases sequences

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.

Residues are the D-channel residues posed in paper – Side view

Glu 17Thr 21Gln 82Gln 86Ser 109Ser 153Thr 156Ser 197Thr 231Ile 235No conservation

Critical residues needed for function of the heme-copper oxidasesK and D channels

X-ray crystal structure of type-A oxidase (Rhodobacter sphaeroides numbering)

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

Ile 235

Ile 235 with all residues within 4 Angstroms of it

There are some other residues within 4 angstroms of Ile 235 that could be playing same role-

Trp 193*Thr 231Pro 234Val 236*Phe 238*Trp 239**= compete conservation