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PDBsum entry 5d4j
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Oxidoreductase
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PDB id
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5d4j
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PDB id:
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Oxidoreductase
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Title:
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Chloride-bound form of a copper nitrite reductase from alcaligenes faecals
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Structure:
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Copper-containing nitrite reductase. Chain: a, b, c. Fragment: unp residues 40-376. Synonym: cu-nir. Engineered: yes
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Source:
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Alcaligenes faecalis. Organism_taxid: 511. Gene: nirk, nir. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Resolution:
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2.00Å
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R-factor:
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0.185
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R-free:
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0.232
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Authors:
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Y.Fukuda,K.M.Tse,T.Nakane,T.Nakatsu,M.Suzuki,M.Sugahara,S.Inoue, F.Yumoto,N.Matsugaki,E.Nango,K.Tono,Y.Joti,T.Kameshima,C.Song, M.Yabashi,O.Nureki,M.E.P.Murphy,T.Inoue,S.Iwata,E.Mizohata
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Key ref:
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Y.Fukuda
et al.
(2016).
Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.
Proc Natl Acad Sci U S A,
113,
2928-2933.
PubMed id:
DOI:
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Date:
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07-Aug-15
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Release date:
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09-Mar-16
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PROCHECK
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Headers
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References
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P38501
(NIR_ALCFA) -
Copper-containing nitrite reductase from Alcaligenes faecalis
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Seq:
Struc:
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376 a.a.
335 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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Enzyme class:
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E.C.1.7.2.1
- nitrite reductase (NO-forming).
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Reaction:
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nitric oxide + Fe(III)-[cytochrome c] + H2O = Fe(II)-[cytochrome c] + nitrite + 2 H+
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nitric oxide
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+
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Fe(III)-[cytochrome c]
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+
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H2O
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=
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Fe(II)-[cytochrome c]
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+
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nitrite
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+
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2
×
H(+)
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Cofactor:
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Cu cation or Fe cation; FAD
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Cu cation
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or
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Fe cation
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FAD
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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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Proc Natl Acad Sci U S A
113:2928-2933
(2016)
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PubMed id:
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Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.
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Y.Fukuda,
K.M.Tse,
T.Nakane,
T.Nakatsu,
M.Suzuki,
M.Sugahara,
S.Inoue,
T.Masuda,
F.Yumoto,
N.Matsugaki,
E.Nango,
K.Tono,
Y.Joti,
T.Kameshima,
C.Song,
T.Hatsui,
M.Yabashi,
O.Nureki,
M.E.Murphy,
T.Inoue,
S.Iwata,
E.Mizohata.
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ABSTRACT
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Proton-coupled electron transfer (PCET), a ubiquitous phenomenon in biological
systems, plays an essential role in copper nitrite reductase (CuNiR), the key
metalloenzyme in microbial denitrification of the global nitrogen cycle.
Analyses of the nitrite reduction mechanism in CuNiR with conventional
synchrotron radiation crystallography (SRX) have been faced with difficulties,
because X-ray photoreduction changes the native structures of metal centers and
the enzyme-substrate complex. Using serial femtosecond crystallography (SFX), we
determined the intact structures of CuNiR in the resting state and the nitrite
complex (NC) state at 2.03- and 1.60-Å resolution, respectively. Furthermore,
the SRX NC structure representing a transient state in the catalytic cycle was
determined at 1.30-Å resolution. Comparison between SRX and SFX structures
revealed that photoreduction changes the coordination manner of the substrate
and that catalytically important His255 can switch hydrogen bond partners
between the backbone carbonyl oxygen of nearby Glu279 and the side-chain
hydroxyl group of Thr280. These findings, which SRX has failed to uncover,
propose a redox-coupled proton switch for PCET. This concept can explain how
proton transfer to the substrate is involved in intramolecular electron transfer
and why substrate binding accelerates PCET. Our study demonstrates the potential
of SFX as a powerful tool to study redox processes in metalloenzymes.
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