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PDBsum entry 3wpm
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Oxidoreductase
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PDB id
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3wpm
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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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Crystal structure of the anaerobic desb-gallate complex by co- crystallization
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Structure:
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Gallate dioxygenase. Chain: a, b. Engineered: yes
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Source:
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Sphingobium. Organism_taxid: 627192. Strain: syk-6. Gene: desb. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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2.50Å
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R-factor:
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0.229
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R-free:
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0.296
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Authors:
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K.Sugimoto,M.Senda,D.Kasai,M.Fukuda,E.Masai,T.Senda
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Key ref:
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K.Sugimoto
et al.
(2014).
Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6.
Plos One,
9,
e92249.
PubMed id:
DOI:
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Date:
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14-Jan-14
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Release date:
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30-Apr-14
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PROCHECK
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Headers
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References
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G2IKE5
(G2IKE5_9SPHN) -
Gallate dioxygenase from Sphingobium sp. (strain NBRC 103272 / SYK-6)
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Seq:
Struc:
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418 a.a.
408 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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DOI no:
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Plos One
9:e92249
(2014)
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PubMed id:
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Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6.
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K.Sugimoto,
M.Senda,
D.Kasai,
M.Fukuda,
E.Masai,
T.Senda.
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ABSTRACT
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DesB, which is derived from Sphingobium sp. SYK-6, is a type II extradiol
dioxygenase that catalyzes a ring opening reaction of gallate. While typical
extradiol dioxygenases show broad substrate specificity, DesB has strict
substrate specificity for gallate. The substrate specificity of DesB seems to be
required for the efficient growth of S. sp. SYK-6 using lignin-derived aromatic
compounds. Since direct coordination of hydroxyl groups of the substrate to the
non-heme iron in the active site is a critical step for the catalytic reaction
of the extradiol dioxygenases, the mechanism of the substrate recognition and
coordination of DesB was analyzed by biochemical and crystallographic methods.
Our study demonstrated that the direct coordination between the non-heme iron
and hydroxyl groups of the substrate requires a large shift of the Fe (II) ion
in the active site. Mutational analysis revealed that His124 and His192 in the
active site are essential to the catalytic reaction of DesB. His124, which
interacts with OH (4) of the bound gallate, seems to contribute to proper
positioning of the substrate in the active site. His192, which is located close
to OH (3) of the gallate, is likely to serve as the catalytic base. Glu377'
interacts with OH (5) of the gallate and seems to play a critical role in the
substrate specificity. Our biochemical and structural study showed the substrate
recognition and catalytic mechanisms of DesB.
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