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PDBsum entry 1cgo
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Electron transport (cytochrome)
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PDB id
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1cgo
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References listed in PDB file
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Key reference
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Title
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Three-Dimensional structure of cytochrome c' From two alcaligenes species and the implications for four-Helix bundle structures.
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Authors
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A.J.Dobbs,
B.F.Anderson,
H.R.Faber,
E.N.Baker.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1996,
52,
356-368.
[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
86%.
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Abstract
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The three-dimensional structures of two cytochromes c' have been determined in
order to analyse the common features of proteins of this family and their
relationship with other four-helix bundle structures. The structure of
cytochrome c' from Alcaligenes sp was determined by molecular replacement
supplemented with the iron anomalous scattering and the use of a single
isomorphous heavy-atom derivative, and was refined using synchrotron data to 1.8
A resolution. The final model, comprising 956 protein atoms (one monomer) and 89
water molecules, has a final R value of 0.188 for all data in the range 20.0-1.8
A resolution (14 673 reflections). The structure of the cytochrome c' from
Alcaligenes denitrificans is isomorphous and essentially identical (r.m.s.
deviation for all atoms 0.36 A). Although its amino-acid sequence has not been
determined chemically, only four differences from that of Alcaligenes sp
cytochrome c' were identified by the X-ray analysis. The final model for
Alcaligenes denitrificans cytochrome c', comprising 953 protein atoms and 75
water molecules, gave a final R factor of 0.167 for all data in the range
20.0-2.15 A (8220 reflections). The cytochrome c' monomer forms a classic
four-helix bundle, determined by the packing of hydrophobic side chains around
the enclosed haem group. There are very few cross-linking hydrogen bonds between
the helices, the principal side-chain hydrogen bonding involving one of the haem
propionates and a conserved Arg residue. The cytochrome c' dimer is created by a
crystallographic twofold axis. Monomer-monomer contacts primarily involve the
two A helices, with size complementarity of side chains in a central
solvent-excluded portion of the interface and hydrogen bonding at the periphery.
Both species have a pyroglutamic acid N-terminal residue. The haem iron is
five-coordinate, 0.32 A out of the haem plane towards the fifth ligand, His120.
The unusual magnetic properties of the Fe atom may be linked to a conserved
basic residue, Arg124, adjacent to His120.
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Figure 1.
Fig. 1. Variation of the crystallographic R factor with resolution for the
cytochromes c' from Alcaligenes sp (full line) and Alcaligenes
denitrificans (broken line). he teoretical variation for coordinate
errors of (a) 0.10, (b) 0.15 and (c) 0.20,~ (Luzzati, 1952) is shown.
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Figure 6.
Fig. 6. Stereoview showing the environment of the conserved Argl2
side chain and te inner of the two haem propionate groups.
Hdrogen bonds are shown with broken ines.
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Figure 14.
IMET . L P A A F P E G
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1996,
52,
356-368)
copyright 1996.
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Secondary reference #1
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Title
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Atomic structure of a cytochrome c' With an unusual ligand-Controlled dimer dissociation at 1.8 a resolution.
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Authors
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Z.Ren,
T.Meyer,
D.E.Mcree.
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Ref.
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J Mol Biol, 1993,
234,
433-445.
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PubMed id
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Secondary reference #2
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Title
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Three-Dimensional structure of ferricytochrome c' From rhodospirillum rubrum at 2.8 a resolution.
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Authors
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M.Yasui,
S.Harada,
Y.Kai,
N.Kasai,
M.Kusunoki,
Y.Matsuura.
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Ref.
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J Biochem (tokyo), 1992,
111,
317-324.
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PubMed id
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Secondary reference #3
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Title
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Structure of ferricytochrome c' From rhodospirillum molischianum at 1.67 a resolution.
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Authors
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B.C.Finzel,
P.C.Weber,
K.D.Hardman,
F.R.Salemme.
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Ref.
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J Mol Biol, 1985,
186,
627-643.
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PubMed id
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Secondary reference #4
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Title
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Crystallographic structure of rhodospirillum molischianum ferricytochrome c' At 2.5 angstroms resolution
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Authors
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P.C.Weber,
A.Howard,
N.H.Xoung,
F.R.Salemme.
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Ref.
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j mol biol, 1981,
353,
399.
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Secondary reference #5
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Title
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The amino acid sequence of cytochrome c' From alcaligenes sp. N.C.I.B. 11015.
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Author
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R.P.Ambler.
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Ref.
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Biochem J, 1973,
135,
751-758.
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PubMed id
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