PDBsum entry 3cxh

Oxidoreductase

PDB id: 3cxh

Contents

Protein chains

431 a.a. *

352 a.a. *

385 a.a. *

246 a.a. *

185 a.a. *

74 a.a. *

125 a.a. *

93 a.a. *

55 a.a. *

127 a.a. *

107 a.a. *

112 a.a. *

Ligands

GLC-FRU

UMQ ×2

HEM ×7

SMA ×2

8PE ×2

CN6 ×2

9PE ×2

7PH ×2

FES ×2

6PH ×2

Waters ×548

* Residue conservation analysis

PDB id:

3cxh

Name:

Oxidoreductase

Title:

Structure of yeast complex iii with isoform-2 cytochromE C bound and definition of a minimal core interface for electron transfer.

Structure:

Cytochrome b-c1 complex subunit 1, mitochondrial. Chain: a, l. Synonym: ubiquinol- cytochromE-C reductase complex core protein 1, core protein i, complex iii subunit 1. Cytochrome b-c1 complex subunit 2, mitochondrial. Chain: b, m. Synonym: ubiquinol- cytochromE-C reductase complex core protein 2, core protein ii, complex iii subunit 2. Cytochrome b.

Source:

Saccharomyces cerevisiae. Yeast. Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Yeast

Resolution:

2.50Å R-factor: 0.225 R-free: 0.256

Authors:

S.R.N.Solmaz,C.Hunte

Key ref:

S.R.Solmaz and C.Hunte (2008). Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer. J Biol Chem, 283, 17542-17549. PubMed id: 18390544 DOI: 10.1074/jbc.M710126200

Date:

24-Apr-08 Release date: 13-May-08

Protein chains

P07256  (QCR1_YEAST) -  Cytochrome b-c1 complex subunit 1, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 457 a.a.

Struc: 431 a.a.*

Protein chains

P07257  (QCR2_YEAST) -  Cytochrome b-c1 complex subunit 2, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 368 a.a.

Struc: 352 a.a.

Protein chains

P00163  (CYB_YEAST) -  Cytochrome b from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 385 a.a.

Struc: 385 a.a.

Protein chains

P07143  (CY1_YEAST) -  Cytochrome c1, heme protein, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 309 a.a.

Struc: 246 a.a.

Protein chains

P08067  (UCRI_YEAST) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 215 a.a.

Struc: 185 a.a.

Protein chains

P00127  (QCR6_YEAST) -  Cytochrome b-c1 complex subunit 6, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 147 a.a.

Struc: 74 a.a.

Protein chains

P00128  (QCR7_YEAST) -  Cytochrome b-c1 complex subunit 7, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 127 a.a.

Struc: 125 a.a.

Protein chains

P08525  (QCR8_YEAST) -  Cytochrome b-c1 complex subunit 8, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 94 a.a.

Struc: 93 a.a.

Protein chains

P22289  (QCR9_YEAST) -  Cytochrome b-c1 complex subunit 9, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 66 a.a.

Struc: 55 a.a.

Protein chains

No UniProt id for this chain

Struc: 127 a.a.

Protein chains

No UniProt id for this chain

Struc: 107 a.a.

Protein chain

P00045  (CYC7_YEAST) -  Cytochrome c isoform 2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 113 a.a.

Struc: 112 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B, F, G, H, I, L, M, Q, R, S, T: E.C.1.10.2.2 - Transferred entry: 7.1.1.8.
• Reaction: Quinol + 2 ferricytochrome c = quinone + 2 ferrocytochrome c + 2 H⁺

Quinol + 2 × ferricytochrome c = quinone (Bound ligand (Het Group name = GLC) matches with 72.73% similarity) + 2 × ferrocytochrome c + 2 × H(+)

• Enzyme class 3: Chains C, D, E, N, O, P: E.C.7.1.1.8 - quinol--cytochrome-c reductase.
• Reaction: a quinol + 2 Fe(III)-[cytochrome c](out) = a quinone + 2 Fe(II)- [cytochrome c](out) + 2 H(+)(out)
• Enzyme class 4: Chain W: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M710126200

J Biol Chem 283:17542-17549 (2008)

PubMed id: 18390544

Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer.

S.R.Solmaz, C.Hunte.

ABSTRACT

In cellular respiration, cytochrome c transfers electrons from cytochrome bc(1) complex (complex III) to cytochrome c oxidase by transiently binding to the membrane proteins. Here, we report the structure of isoform-1 cytochrome c bound to cytochrome bc(1) complex at 1.9 A resolution in reduced state. The dimer structure is asymmetric. Monovalent cytochrome c binding is correlated with conformational changes of the Rieske head domain and subunit QCR6p and with a higher number of interfacial water molecules bound to cytochrome c(1). Pronounced hydration and a "mobility mismatch" at the interface with disordered charged residues on the cytochrome c side are favorable for transient binding. Within the hydrophobic interface, a minimal core was identified by comparison with the novel structure of the complex with bound isoform-2 cytochrome c. Four core interactions encircle the heme cofactors surrounded by variable interactions. The core interface may be a feature to gain specificity for formation of the reactive complex.

Selected figure(s)

Figure 2.
FIGURE 2. The interface of cyt c (green) and cyt c[1] (pink) at high resolution. Hemes, black; water molecules, cyan. A, 2F[o] - F[c] electron density map at the interface, contoured at 1 and drawn as a blue mesh. B, stereo view of the core interface. The minimal core interface (dashed lines) is defined by four residue pairs (labeled) that were identified in three structures of the electron transfer complex. The contact of the heme CBC atoms is shown as a dotted line.

Figure 3.
FIGURE 3. The building blocks of the interface. The cyt c[1] (A)-cyt c (B) interface is shown in open book view. The heme groups (black) are encircled by the core interface (orange area, interacting atoms as orange spheres). The variable interface (yellow) surrounds the latter. Residues mediating long-range electrostatic interactions (pink and blue for negative and positive charges, respectively) form a semicircle around the central hydrophobic contact site. C, the semitransparent surface representation of cyt c[1] (gray) and cyt c (green) shows the position of these long-range electrostatic interactions in the high resolution structure (Table 1) as highlighted in blue-green and pink (positive and negative charges, respectively). Heme groups are shown in black. A high number of water molecules (cyan spheres) are bound at the interface of cyt c[1] (D) but not of cyt c (E). Only two of these water molecules form hydrogen bonds to both cyt c[1] and cyt c (green spheres). F, interface water molecules bound to cyt c[1] colored in cyan and green (as in D) are superimposed with all surface water molecules that are present at the other cyt c[1] with the non-occupied cyt c binding site (dark blue spheres). Surface water molecules up to a distance of 3.5 Å are included.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 17542-17549) copyright 2008.

Figures were selected by the author.