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PDBsum entry 1bvb
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Electron transport
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PDB id
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1bvb
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Contents |
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* Residue conservation analysis
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DOI no:
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Nat Struct Biol
5:1005-1012
(1998)
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PubMed id:
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Heme packing motifs revealed by the crystal structure of the tetra-heme cytochrome c554 from Nitrosomonas europaea.
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T.M.Iverson,
D.M.Arciero,
B.T.Hsu,
M.S.Logan,
A.B.Hooper,
D.C.Rees.
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ABSTRACT
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Cytochrome c554 (cyt c554), a tetra-heme cytochrome from Nitrosomonas europaea,
is an essential component in the biological nitrification pathway. In N.
europaea, ammonia is converted to hydroxylamine, which is then oxidized to
nitrite by hydroxylamine oxidoreductase (HAO). Cyt c554 functions in the latter
process by accepting pairs of electrons from HAO and transferring them to a
cytochrome acceptor. The crystal structure of cyt c554 at 2.6 A resolution shows
a predominantly alpha-helical protein with four covalently attached hemes. The
four hemes are arranged in two pairs such that the planes of the porphyrin rings
are almost parallel and overlapping at the edge; corresponding heme arrangements
are observed in other multi-heme proteins. Striking structural similarities are
evident between the tetra-heme core of cyt c554 and hemes 3-6 of HAO, which
suggests an evolutionary relationship between these redox partners.
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Selected figure(s)
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Figure 1.
Figure 1. The oxidation of NH[3] to NO[2]^− by Nitrosomonas
europaea. Ammonia is first oxidized to hydroxylamine
(NH[2]OH) by ammonia monooxygenase (AMO.) The product, NH[2]OH,
is oxidized to NO[ 2]^− by HAO. The released electrons are
transferred to cyt c554 (a two electron acceptor) and then
possibly to cyt c552 (a one electron acceptor), which ultimately
passes electrons to terminal oxidases. The electron transfer
pathway following the oxidation of NH[2]OH to NO[2]^− is not
fully understood and alternative electron transfer routes may
exist^30, including the transfer of electrons from cyt c554
directly to a membrane-bound electron transport chain^31.
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Figure 3.
Figure 3. Heme configuration and superposition of heme stacking
motifs. a, Inter-heme iron distances and overall heme
configuration. Hemes are shown in the same view as in Fig. 2a.
b, Overlay of hemes I and III from cyt c554 (red) with hemes 1
and 2 from HAO (teal), hemes 3 and 5 from HAO (magenta), hemes 6
and 7 from HAO (green) and hemes 1 and 2 from the split Soret
cytochrome (yellow). The pseudo two-fold axis has been
calculated for the hemes of cyt c554 and is shown as a black
line. c, Overlay of hemes II and IV from cyt c554 (red) with
P460 and 6 of HAO (teal). The 5-coordinate hemes II (cyt c554)
and P460 (HAO) are on the right. The pseudo two-fold axis
calculated for hemes II and IV of cyt c554 is indicated as a
black line. d, Overlay of the two central hemes, hemes III and
IV, from cyt c554 with hemes 5 and 6 from HAO (teal), hemes 7
and 8 from HAO (green), hemes 69 and 70 from cyt c551.5
(magenta) and hemes 201 and 203 from cyt c[3] (yellow). e,
Stereoview of the overlay of all hemes and surrounding
structural elements from cyt c554 (red) with hemes 3−6 of HAO
(teal).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(1998,
5,
1005-1012)
copyright 1998.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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C.Lockwood,
J.N.Butt,
T.A.Clarke,
and
D.J.Richardson
(2011).
Molecular interactions between multihaem cytochromes: probing the protein-protein interactions between pentahaem cytochromes of a nitrite reductase complex.
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Biochem Soc Trans,
39,
263-268.
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L.J.Smith,
A.Kahraman,
and
J.M.Thornton
(2010).
Heme proteins--diversity in structural characteristics, function, and folding.
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Proteins,
78,
2349-2368.
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D.Heitmann,
and
O.Einsle
(2008).
Pseudo-merohedral twinning in crystals of the dihaem c-type cytochrome DHC2 from Geobacter sulfurreducens.
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Acta Crystallogr D Biol Crystallogr,
64,
993-999.
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H.J.Kim,
A.Zatsman,
A.K.Upadhyay,
M.Whittaker,
D.Bergmann,
M.P.Hendrich,
and
A.B.Hooper
(2008).
Membrane tetraheme cytochrome c(m552) of the ammonia-oxidizing nitrosomonas europaea: a ubiquinone reductase.
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Biochemistry,
47,
6539-6551.
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J.Kostera,
M.D.Youngblut,
J.M.Slosarczyk,
and
A.A.Pacheco
(2008).
Kinetic and product distribution analysis of NO* reductase activity in Nitrosomonas europaea hydroxylamine oxidoreductase.
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J Biol Inorg Chem,
13,
1073-1083.
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W.Liu,
C.E.Rogge,
G.F.da Silva,
V.P.Shinkarev,
A.L.Tsai,
Y.Kamensky,
G.Palmer,
and
R.J.Kulmacz
(2008).
His92 and His110 selectively affect different heme centers of adrenal cytochrome b(561).
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Biochim Biophys Acta,
1777,
1218-1228.
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D.J.Arp,
P.S.Chain,
and
M.G.Klotz
(2007).
The impact of genome analyses on our understanding of ammonia-oxidizing bacteria.
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Annu Rev Microbiol,
61,
503-528.
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A.K.Upadhyay,
A.B.Hooper,
and
M.P.Hendrich
(2006).
NO reductase activity of the tetraheme cytochrome C554 of Nitrosomonas europaea.
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J Am Chem Soc,
128,
4330-4337.
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M.L.Rodrigues,
T.F.Oliveira,
I.A.Pereira,
and
M.Archer
(2006).
X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination.
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EMBO J,
25,
5951-5960.
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PDB code:
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R.E.Di Paolo,
P.M.Pereira,
I.Gomes,
F.M.Valente,
I.A.Pereira,
and
R.Franco
(2006).
Resonance Raman fingerprinting of multiheme cytochromes from the cytochrome c3 family.
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J Biol Inorg Chem,
11,
217-224.
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C.G.Mowat,
and
S.K.Chapman
(2005).
Multi-heme cytochromes--new structures, new chemistry.
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Dalton Trans,
(),
3381-3389.
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D.J.Bergmann,
A.B.Hooper,
and
M.G.Klotz
(2005).
Structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history.
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Appl Environ Microbiol,
71,
5371-5382.
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J.Alric,
Y.Pierre,
D.Picot,
J.Lavergne,
and
F.Rappaport
(2005).
Spectral and redox characterization of the heme ci of the cytochrome b6f complex.
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Proc Natl Acad Sci U S A,
102,
15860-15865.
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K.S.Bender,
C.Shang,
R.Chakraborty,
S.M.Belchik,
J.D.Coates,
and
L.A.Achenbach
(2005).
Identification, characterization, and classification of genes encoding perchlorate reductase.
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J Bacteriol,
187,
5090-5096.
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R.Chelli,
F.L.Gervasio,
P.Procacci,
and
V.Schettino
(2004).
Inter-residue and solvent-residue interactions in proteins: a statistical study on experimental structures.
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Proteins,
55,
139-151.
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F.A.Rotsaert,
B.M.Hallberg,
S.de Vries,
P.Moenne-Loccoz,
C.Divne,
V.Renganathan,
and
M.H.Gold
(2003).
Biophysical and structural analysis of a novel heme B iron ligation in the flavocytochrome cellobiose dehydrogenase.
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J Biol Chem,
278,
33224-33231.
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PDB code:
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A.Brigé,
D.Leys,
T.E.Meyer,
M.A.Cusanovich,
and
J.J.Van Beeumen
(2002).
The 1.25 A resolution structure of the diheme NapB subunit of soluble nitrate reductase reveals a novel cytochrome c fold with a stacked heme arrangement.
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Biochemistry,
41,
4827-4836.
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PDB code:
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D.Leys,
T.E.Meyer,
A.S.Tsapin,
K.H.Nealson,
M.A.Cusanovich,
and
J.J.Van Beeumen
(2002).
Crystal structures at atomic resolution reveal the novel concept of "electron-harvesting" as a role for the small tetraheme cytochrome c.
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J Biol Chem,
277,
35703-35711.
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PDB codes:
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M.Paoli,
J.Marles-Wright,
and
A.Smith
(2002).
Structure-function relationships in heme-proteins.
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DNA Cell Biol,
21,
271-280.
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V.A.Bamford,
H.C.Angove,
H.E.Seward,
A.J.Thomson,
J.A.Cole,
J.N.Butt,
A.M.Hemmings,
and
D.J.Richardson
(2002).
Structure and spectroscopy of the periplasmic cytochrome c nitrite reductase from Escherichia coli.
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Biochemistry,
41,
2921-2931.
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PDB code:
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L.Poughon,
C.G.Dussap,
and
J.B.Gros
(2001).
Energy model and metabolic flux analysis for autotrophic nitrifiers.
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Biotechnol Bioeng,
72,
416-433.
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O.Einsle,
S.Foerster,
K.Mann,
G.Fritz,
A.Messerschmidt,
and
P.M.Kroneck
(2001).
Spectroscopic investigation and determination of reactivity and structure of the tetraheme cytochrome c3 from Desulfovibrio desulfuricans Essex 6.
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Eur J Biochem,
268,
3028-3035.
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PDB code:
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P.N.da Costa,
P.E.Marujo,
W.M.van Dongen,
C.M.Arraiano,
and
L.M.Saraiva
(2000).
Cloning, sequencing and expression of the tetraheme cytochrome c(3) from Desulfovibrio gigas.
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Biochim Biophys Acta,
1492,
271-275.
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S.J.Field,
P.S.Dobbin,
M.R.Cheesman,
N.J.Watmough,
A.J.Thomson,
and
D.J.Richardson
(2000).
Purification and magneto-optical spectroscopic characterization of cytoplasmic membrane and outer membrane multiheme c-type cytochromes from Shewanella frigidimarina NCIMB400.
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J Biol Chem,
275,
8515-8522.
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D.J.Richardson,
and
N.J.Watmough
(1999).
Inorganic nitrogen metabolism in bacteria.
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Curr Opin Chem Biol,
3,
207-219.
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P.D.Barker,
and
S.J.Ferguson
(1999).
Still a puzzle: why is haem covalently attached in c-type cytochromes?
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Structure,
7,
R281-R290.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
