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PDBsum entry 2c8s
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Electron transport
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PDB id
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2c8s
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References listed in PDB file
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Key reference
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Title
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The 1.6a X-Ray structure of the unusual c-Type cytochrome, Cytochrome cl, From the methylotrophic bacterium methylobacterium extorquens.
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Authors
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P.Williams,
L.Coates,
F.Mohammed,
R.Gill,
P.Erskine,
D.Bourgeois,
S.P.Wood,
C.Anthony,
J.B.Cooper.
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Ref.
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J Mol Biol, 2006,
357,
151-162.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
81%.
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Abstract
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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.
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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).
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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.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
357,
151-162)
copyright 2006.
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