PDBsum entry 2c8s

Electron transport

PDB id: 2c8s

Contents

Protein chain

149 a.a. *

Ligands

HEM

Metals

_CA

Waters ×143

* Residue conservation analysis

PDB id:

2c8s

Name:

Electron transport

Title:

Cytochrome cl from methylobacterium extorquens

Structure:

CytochromE C-l. Chain: a

Source:

Methylobacterium extorquens. Organism_taxid: 408

Resolution:

1.60Å R-factor: 0.210 R-free: 0.250

Authors:

P.A.Williams,L.Coates,F.Mohammed,R.Gill,P.T.Erskine,S.P.Wood J, B.Cooper,C.Anthony

Key ref:

P.Williams et al. (2006). The 1.6A X-ray structure of the unusual c-type cytochrome, cytochrome cL, from the methylotrophic bacterium Methylobacterium extorquens. J Mol Biol, 357, 151-162. PubMed id: 16414073 DOI: 10.1016/j.jmb.2005.12.055

Date:

06-Dec-05 Release date: 08-Dec-05

Supersedes:

1umm

Protein chain

P14774  (CYCL_METEA) -  Cytochrome c-L from Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)

Seq: 197 a.a.

Struc: 149 a.a.

DOI no: 10.1016/j.jmb.2005.12.055

J Mol Biol 357:151-162 (2006)

PubMed id: 16414073

The 1.6A X-ray structure of the unusual c-type cytochrome, cytochrome cL, from the methylotrophic bacterium Methylobacterium extorquens.

P.Williams, L.Coates, F.Mohammed, R.Gill, P.Erskine, D.Bourgeois, S.P.Wood, C.Anthony, J.B.Cooper.

ABSTRACT

The structure of cytochrome cL from Methylobacterium extorquens has been determined by X-ray crystallography to a resolution of 1.6 A. This unusually large, acidic cytochrome is the physiological electron acceptor for the quinoprotein methanol dehydrogenase in the periplasm of methylotrophic bacteria. Its amino acid sequence is completely different from that of other cytochromes but its X-ray structure reveals a core that is typical of class I cytochromes c, having alpha-helices folded into a compact structure enclosing the single haem c prosthetic group and leaving one edge of the haem exposed. The haem is bound through thioether bonds to Cys65 and Cys68, and the fifth ligand to the haem iron is provided by His69. Remarkably, the sixth ligand is provided by His112, and not by Met109, which had been shown to be the sixth ligand in solution. Cytochrome cL is unusual in having a disulphide bridge that tethers the long C-terminal extension to the body of the structure. The crystal structure reveals that, close to the inner haem propionate, there is tightly bound calcium ion that is likely to be involved in stabilization of the redox potential, and that may be important in the flow of electrons from reduced pyrroloquinoline quinone in methanol dehydrogenase to the haem of cytochrome cL. As predicted, both haem propionates are exposed to solvent, accounting for the unusual influence of pH on the redox potential of this cytochrome.

Selected figure(s)

Figure 2.
Figure 2. (a) The main structural features of cytochrome c[L]. Although there is no sequence identity with other cytochromes, the helices A, C and E constitute the typical haem-enclosing fold seen in all cytochromes c. Helices are labelled HelA, HelB, etc. Loop 1 (grey) joins the N-terminal helix and helix A; loop 2 (purple) between helix A and helix B, carries the haem-binding sequence and the amino acid residues that coordinate to the calcium ion; loop 3 (orange) is the exceptionally flexible loop that joins helix C to helix E, and carries the sixth ligand to the haem (His112) and the methionine (Met109) that is the sixth ligand in solution. The red sphere is the iron atom at the centre of the haem prosthetic group. HP6 is the outer haem propionate group and HP7 is the inner haem propionate group. The blue spheres are the water molecules (Wat6-Wat9) that coordinate to the calcium ion (magenta sphere). Met109 is the residue that forms the sixth ligand to the haem in solutions of the cytochrome. (b) The main structural features of cytochrome c[L] (stereo view). The elements of this structure are as indicated in (a).

Figure 6.
Figure 6. Comparison of the main structural components in cytochrome c[L] and in its homologue cytochrome c[551i]. The single letters (A-G, and N) indicate the a helices. The haem is represented with space-filling atoms. The loops are labelled L1-L6. The first 13 residues are missing from the cytochrome c[L] and the next 11 residues are not seen in the crystal structure. In the homologous cytochrome c[551i] all residues are present in the N-terminal loop (shown in green) in the crystal structure, in which they interact with loop 3 (L3; orange) protecting it from exposure to solvent; it is this interaction that is absent from cytochrome c[L], leading to an increased flexibility of loop 3 (Figure 3) and the replacement of Met109 by His112 in the crystal structure. The last eight residues of cytochrome c[551i] are not seen in the structure.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 151-162) copyright 2006.

Figures were selected by an automated process.