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PDBsum entry 4zxd
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Oxidoreductase
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PDB id
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4zxd
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References listed in PDB file
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Key reference
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Title
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Crystal structure of pnpcd, A two-Subunit hydroquinone 1,2-Dioxygenase, Reveals a novel structural class of fe2+-Dependent dioxygenases.
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Authors
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S.Liu,
T.Su,
C.Zhang,
W.M.Zhang,
D.Zhu,
J.Su,
T.Wei,
K.Wang,
Y.Huang,
L.Guo,
S.Xu,
N.Y.Zhou,
L.Gu.
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Ref.
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J Biol Chem, 2015,
290,
24547-24560.
[DOI no: ]
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PubMed id
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Abstract
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Aerobic microorganisms have evolved a variety of pathways to degrade aromatic
and heterocyclic compounds. However, only several classes of oxygenolytic
fission reaction have been identified for the critical ring cleavage
dioxygenases. Among them, the most well studied dioxygenases proceed via
catecholic intermediates, followed by noncatecholic hydroxy-substituted aromatic
carboxylic acids. Therefore, the recently reported hydroquinone 1,2-dioxygenases
add to the diversity of ring cleavage reactions. Two-subunit hydroquinone
1,2-dioxygenase PnpCD, the key enzyme in the hydroquinone pathway of
para-nitrophenol degradation, catalyzes the ring cleavage of hydroquinone to
γ-hydroxymuconic semialdehyde. Here, we report three PnpCD structures, named
apo-PnpCD, PnpCD-Fe(3+), and PnpCD-Cd(2+)-HBN (substrate analog
hydroxyenzonitrile), respectively. Structural analysis showed that both the PnpC
and the C-terminal domains of PnpD comprise a conserved cupin fold, whereas PnpC
cannot form a competent metal binding pocket as can PnpD cupin. Four residues of
PnpD (His-256, Asn-258, Glu-262, and His-303) were observed to coordinate the
iron ion. The Asn-258 coordination is particularly interesting because this
coordinating residue has never been observed in the homologous cupin structures
of PnpCD. Asn-258 is proposed to play a pivotal role in binding the iron prior
to the enzymatic reaction, but it might lose coordination to the iron when the
reaction begins. PnpD also consists of an intriguing N-terminal domain that
might have functions other than nucleic acid binding in its structural homologs.
In summary, PnpCD has no apparent evolutionary relationship with other
iron-dependent dioxygenases and therefore defines a new structural class. The
study of PnpCD might add to the understanding of the ring cleavage of
dioxygenases.
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