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PDBsum entry 2nap
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Oxidoreductase
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PDB id
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2nap
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Oxidoreductase
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Title:
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Dissimilatory nitrate reductase (nap) from desulfovibrio desulfuricans
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Structure:
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Protein (periplasmic nitrate reductase). Chain: a
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Source:
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Desulfovibrio desulfuricans. Organism_taxid: 876. Collection: atcc 27774. Cellular_location: periplasm
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Resolution:
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1.90Å
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R-factor:
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0.218
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R-free:
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0.267
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Authors:
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J.M.Dias,M.Than,A.Humm,R.Huber,G.Bourenkov,H.Bartunik,S.Bursakov, J.Calvete,J.Caldeira,C.Carneiro,J.Moura,I.Moura,M.J.Romao
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Key ref:
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J.M.Dias
et al.
(1999).
Crystal structure of the first dissimilatory nitrate reductase at 1.9 A solved by MAD methods.
Structure,
7,
65-79.
PubMed id:
DOI:
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Date:
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18-Sep-98
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Release date:
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19-Sep-99
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PROCHECK
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Headers
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References
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P81186
(NAPA_DESDA) -
Periplasmic nitrate reductase from Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB)
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Seq:
Struc:
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755 a.a.
720 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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Enzyme class:
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E.C.1.9.6.1
- nitrate reductase (cytochrome).
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Reaction:
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2 Fe(II)-[cytochrome] + nitrate + 2 H+ = 2 Fe(III)-[cytochrome] + nitrite + H2O
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2
×
Fe(II)-[cytochrome]
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+
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nitrate
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+
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2
×
H(+)
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=
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2
×
Fe(III)-[cytochrome]
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+
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nitrite
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+
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H2O
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Structure
7:65-79
(1999)
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PubMed id:
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Crystal structure of the first dissimilatory nitrate reductase at 1.9 A solved by MAD methods.
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J.M.Dias,
M.E.Than,
A.Humm,
R.Huber,
G.P.Bourenkov,
H.D.Bartunik,
S.Bursakov,
J.Calvete,
J.Caldeira,
C.Carneiro,
J.J.Moura,
I.Moura,
M.J.Romão.
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ABSTRACT
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BACKGROUND: The periplasmic nitrate reductase (NAP) from the sulphate reducing
bacterium Desulfovibrio desulfuricans ATCC 27774 is induced by growth on nitrate
and catalyses the reduction of nitrate to nitrite for respiration. NAP is a
molybdenum-containing enzyme with one bis-molybdopterin guanine dinucleotide
cluster in a single polypeptide chain of 723
amino acid residues. To date, there is no crystal structure of a nitrate
reductase. RESULTS: The first crystal structure of a dissimilatory (respiratory)
nitrate reductase was determined at 1.9 A resolution by multiwavelength
anomalous diffraction (MAD) methods. The structure is folded into four domains
with an alpha/beta-type topology and all four domains are involved in cofactor
centre is located near the periphery of the molecule,
whereas the MGD cofactor extends across the interior of the molecule interacting
with residues from all four domains. The molybdenum atom is located at the
cluster.
The structure of NAP reveals the details of the catalytic molybdenum site, which
is coordinated to two MGD cofactors, Cys140, and a water/hydroxo ligand. A
facile electron-transfer pathway through bonds connects the molybdenum and the
cluster. CONCLUSIONS: The polypeptide fold of NAP and the arrangement
of the cofactors is related to that of Escherichia coli formate dehydrogenase
(FDH) and distantly resembles dimethylsulphoxide reductase. The close structural
homology of NAP and FDH shows how small changes in the vicinity of the
molybdenum catalytic site are sufficient for the substrate specificity.
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Selected figure(s)
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Figure 3.
Figure 3. The overall fold of NAP. (a) Stereoview of the
structure of NAP from Desulfovibrio desulfuricans ATCC 27774
with the different domains coloured: domain I (residues 4–61,
464–492 and 517–561) in red; domain II (residues 62–135,
347–463 and 493–516) in green; domain III (residues
136–346) in yellow; and domain IV (residues 562–723) in
blue. The funnel-like cavity, which provides access to the
molybdenum catalytic site, can be seen on the upper part of the
molecule between domains II and III. (b) Stereoview Cα trace
of NAP for domains I and III with residues labelled. (c)
Stereoview Cα trace of NAP for domains II and IV with residues
labelled. The MGD cofactors and the [4Fe–4S] cluster are shown
in ball-and-stick representation. (Figures were prepared with
the programs MOLSCRIPT [75] and Raster-3D [76].)
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1999,
7,
65-79)
copyright 1999.
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Figure was
selected
by the author.
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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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S.O.Dahms,
M.Kuester,
C.Streb,
C.Roth,
N.Sträter,
and
M.E.Than
(2013).
Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement.
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Acta Crystallogr D Biol Crystallogr,
69,
284-297.
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C.Coelho,
P.J.González,
J.G.Moura,
I.Moura,
J.Trincão,
and
M.João Romão
(2011).
The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states.
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J Mol Biol,
408,
932-948.
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PDB codes:
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E.Cremades,
J.Echeverría,
and
S.Alvarez
(2010).
The trigonal prism in coordination chemistry.
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Chemistry,
16,
10380-10396.
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M.D.Miller,
L.Aravind,
C.Bakolitsa,
C.L.Rife,
D.Carlton,
P.Abdubek,
T.Astakhova,
H.L.Axelrod,
H.J.Chiu,
T.Clayton,
M.C.Deller,
L.Duan,
J.Feuerhelm,
J.C.Grant,
G.W.Han,
L.Jaroszewski,
K.K.Jin,
H.E.Klock,
M.W.Knuth,
P.Kozbial,
S.S.Krishna,
A.Kumar,
D.Marciano,
D.McMullan,
A.T.Morse,
E.Nigoghossian,
L.Okach,
R.Reyes,
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D.Weekes,
Q.Xu,
K.O.Hodgson,
J.Wooley,
M.A.Elsliger,
A.M.Deacon,
A.Godzik,
S.A.Lesley,
and
I.A.Wilson
(2010).
Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
66,
1167-1173.
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PDB code:
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A.Majumdar,
K.Pal,
and
S.Sarkar
(2009).
Necessity of fine tuning in Mo(iv) bis(dithiolene) complexes to warrant nitrate reduction.
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Dalton Trans,
(),
1927-1938.
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J.B.Glass,
F.Wolfe-Simon,
and
A.D.Anbar
(2009).
Coevolution of metal availability and nitrogen assimilation in cyanobacteria and algae.
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Geobiology,
7,
100-123.
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M.Hofmann
(2009).
Density functional theory study of model complexes for the revised nitrate reductase active site in Desulfovibrio desulfuricans NapA.
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J Biol Inorg Chem,
14,
1023-1035.
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M.J.Romão
(2009).
Molybdenum and tungsten enzymes: a crystallographic and mechanistic overview.
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Dalton Trans,
(),
4053-4068.
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N.M.Cerqueira,
P.J.Gonzalez,
C.D.Brondino,
M.J.Romão,
C.C.Romão,
I.Moura,
and
J.J.Moura
(2009).
The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase.
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J Comput Chem,
30,
2466-2484.
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R.J.Alcántara-Hernández,
C.Valenzuela-Encinas,
R.Marsch,
and
L.Dendooven
(2009).
Respiratory and dissimilatory nitrate-reducing communities from an extreme saline alkaline soil of the former lake Texcoco (Mexico).
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Extremophiles,
13,
169-178.
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S.Groysman,
and
R.H.Holm
(2009).
Biomimetic chemistry of iron, nickel, molybdenum, and tungsten in sulfur-ligated protein sites.
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Biochemistry,
48,
2310-2320.
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C.Correia,
S.Besson,
C.D.Brondino,
P.J.González,
G.Fauque,
J.Lampreia,
I.Moura,
and
J.J.Moura
(2008).
Biochemical and spectroscopic characterization of the membrane-bound nitrate reductase from Marinobacter hydrocarbonoclasticus 617.
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J Biol Inorg Chem,
13,
1321-1333.
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S.Najmudin,
P.J.González,
J.Trincão,
C.Coelho,
A.Mukhopadhyay,
N.M.Cerqueira,
C.C.Romão,
I.Moura,
J.J.Moura,
C.D.Brondino,
and
M.J.Romão
(2008).
Periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum.
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J Biol Inorg Chem,
13,
737-753.
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PDB codes:
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Y.Zhang,
and
V.N.Gladyshev
(2008).
Molybdoproteomes and evolution of molybdenum utilization.
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J Mol Biol,
379,
881-899.
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B.J.Jepson,
S.Mohan,
T.A.Clarke,
A.J.Gates,
J.A.Cole,
C.S.Butler,
J.N.Butt,
A.M.Hemmings,
and
D.J.Richardson
(2007).
Spectropotentiometric and structural analysis of the periplasmic nitrate reductase from Escherichia coli.
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J Biol Chem,
282,
6425-6437.
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PDB code:
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C.Coelho,
P.J.González,
J.Trincão,
A.L.Carvalho,
S.Najmudin,
T.Hettman,
S.Dieckman,
J.J.Moura,
I.Moura,
and
M.J.Romão
(2007).
Heterodimeric nitrate reductase (NapAB) from Cupriavidus necator H16: purification, crystallization and preliminary X-ray analysis.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
516-519.
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and
R.A.Zvyagilskaya
(2007).
Nitrate reductases: structure, functions, and effect of stress factors.
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Biochemistry (Mosc),
72,
1151-1160.
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G.B.Seiffert,
G.M.Ullmann,
A.Messerschmidt,
B.Schink,
P.M.Kroneck,
and
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(2007).
Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase.
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Proc Natl Acad Sci U S A,
104,
3073-3077.
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PDB code:
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K.Pal,
P.K.Chaudhury,
and
S.Sarkar
(2007).
Structure of the Michaelis complex and function of the catalytic center in the reductive half-reaction of computational and synthetic models of sulfite oxidase.
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Chem Asian J,
2,
956-964.
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M.Hofmann
(2007).
Density functional theory studies of model complexes for molybdenum-dependent nitrate reductase active sites.
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J Biol Inorg Chem,
12,
989.
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M.Zhao,
X.Jia,
C.Wang,
Q.Li,
K.Zhou,
L.Wang,
H.Liu,
and
S.Peng
(2007).
PAK: an essential motif for forming beta-turn structures and exhibiting the thrombolytic effect of P6A and its analogs.
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Biochem Cell Biol,
85,
730-740.
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X.Ma,
C.Schulzke,
H.G.Schmidt,
and
M.Noltemeyer
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Structural, electrochemical and oxygen atom transfer properties of a molybdenum selenoether complex [Mo2O4(OC3H6SeC3H6O)2] and its thioether analogue [Mo2O4(OC3H6SC3H6O)2].
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Dalton Trans,
(),
1773-1780.
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D.P.Kloer,
C.Hagel,
J.Heider,
and
G.E.Schulz
(2006).
Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum.
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Structure,
14,
1377-1388.
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PDB code:
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J.F.Stolz,
P.Basu,
J.M.Santini,
and
R.S.Oremland
(2006).
Arsenic and selenium in microbial metabolism.
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Annu Rev Microbiol,
60,
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J.Lalucat,
A.Bennasar,
R.Bosch,
E.García-Valdés,
and
N.J.Palleroni
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Biology of Pseudomonas stutzeri.
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Microbiol Mol Biol Rev,
70,
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N.Russo,
M.Toscano,
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T.A.Wesolowski
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Mechanism of nitrate reduction by Desulfovibrio desulfuricans nitrate reductase--a theoretical investigation.
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Chemistry,
12,
2532-2541.
|
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P.J.González,
M.G.Rivas,
C.D.Brondino,
S.A.Bursakov,
I.Moura,
and
J.J.Moura
(2006).
EPR and redox properties of periplasmic nitrate reductase from Desulfovibrio desulfuricans ATCC 27774.
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J Biol Inorg Chem,
11,
609-616.
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A.Marietou,
D.Richardson,
J.Cole,
and
S.Mohan
(2005).
Nitrate reduction by Desulfovibrio desulfuricans: a periplasmic nitrate reductase system that lacks NapB, but includes a unique tetraheme c-type cytochrome, NapM.
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FEMS Microbiol Lett,
248,
217-225.
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C.Noriega,
D.J.Hassett,
and
J.J.Rowe
(2005).
The mobA gene is required for assimilatory and respiratory nitrate reduction but not xanthine dehydrogenase activity in Pseudomonas aeruginosa.
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Curr Microbiol,
51,
419-424.
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E.Nakamaru-Ogiso,
T.Yano,
T.Yagi,
and
T.Ohnishi
(2005).
Characterization of the iron-sulfur cluster N7 (N1c) in the subunit NuoG of the proton-translocating NADH-quinone oxidoreductase from Escherichia coli.
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J Biol Chem,
280,
301-307.
|
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B.J.Jepson,
L.J.Anderson,
L.M.Rubio,
C.J.Taylor,
C.S.Butler,
E.Flores,
A.Herrero,
J.N.Butt,
and
D.J.Richardson
(2004).
Tuning a nitrate reductase for function. The first spectropotentiometric characterization of a bacterial assimilatory nitrate reductase reveals novel redox properties.
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J Biol Chem,
279,
32212-32218.
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J.J.Moura,
C.D.Brondino,
J.Trincão,
and
M.J.Romão
(2004).
Mo and W bis-MGD enzymes: nitrate reductases and formate dehydrogenases.
|
| |
J Biol Inorg Chem,
9,
791-799.
|
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L.Loschi,
S.J.Brokx,
T.L.Hills,
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M.G.Bertero,
A.L.Lovering,
J.H.Weiner,
and
N.C.Strynadka
(2004).
Structural and biochemical identification of a novel bacterial oxidoreductase.
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J Biol Chem,
279,
50391-50400.
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PDB codes:
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O.Einsle,
and
P.M.Kroneck
(2004).
Structural basis of denitrification.
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| |
Biol Chem,
385,
875-883.
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T.Tomiki,
and
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(2004).
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| |
J Mol Evol,
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C.A.Cunha,
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J.M.Dias,
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L.L.Goncalves,
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J.J.Moura,
I.Moura,
and
M.J.Romão
(2003).
Cytochrome c nitrite reductase from Desulfovibrio desulfuricans ATCC 27774. The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA).
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J Biol Chem,
278,
17455-17465.
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PDB code:
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J.Simon,
M.Sänger,
S.C.Schuster,
and
R.Gross
(2003).
Electron transport to periplasmic nitrate reductase (NapA) of Wolinella succinogenes is independent of a NapC protein.
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| |
Mol Microbiol,
49,
69-79.
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M.Jormakka,
B.Byrne,
and
S.Iwata
(2003).
Formate dehydrogenase--a versatile enzyme in changing environments.
|
| |
Curr Opin Struct Biol,
13,
418-423.
|
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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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C.A.McDevitt,
P.Hugenholtz,
G.R.Hanson,
and
A.G.McEwan
(2002).
Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes.
|
| |
Mol Microbiol,
44,
1575-1587.
|
|
|
|
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|
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H.Raaijmakers,
S.Macieira,
J.M.Dias,
S.Teixeira,
S.Bursakov,
R.Huber,
J.J.Moura,
I.Moura,
and
M.J.Romão
(2002).
Gene sequence and the 1.8 A crystal structure of the tungsten-containing formate dehydrogenase from Desulfovibrio gigas.
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| |
Structure,
10,
1261-1272.
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PDB code:
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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
codes are
shown on the right.
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|
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