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PDBsum entry 6k40
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Oxidoreductase
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PDB id
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6k40
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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 alkyl hydroperoxide reductase from d. Radiodurans r1
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Structure:
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Alkyl hydroperoxide reductase ahpd. Chain: a, b, c, d, e, g, f, h, i, j, k, l. Engineered: yes
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Source:
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Deinococcus radiodurans r1. Organism_taxid: 243230. Strain: r1. Gene: dr_1765. Expressed in: escherichia coli. Expression_system_taxid: 562
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Resolution:
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2.27Å
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R-factor:
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0.209
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R-free:
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0.239
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Authors:
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M.-K.Kim,J.Zhang,L.Zhao
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Key ref:
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L.Zhao
et al.
(2020).
Crystal structure of the AhpD-like protein DR1765 from Deinococcus radiodurans R1.
Biochem Biophys Res Commun,
529,
444-449.
PubMed id:
DOI:
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Date:
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22-May-19
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Release date:
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27-May-20
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PROCHECK
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Headers
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References
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Q9RTJ7
(Q9RTJ7_DEIRA) -
Carboxymuconolactone decarboxylase-like domain-containing protein from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)
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Seq:
Struc:
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219 a.a.
186 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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Enzyme class:
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E.C.1.11.1.15
- Transferred entry: 1.11.1.24, 1.11.1.25, 1.11.1.26, 1.11.1.27, 1.11.1.28
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Pathway:
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Peroxiredoxin
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Reaction:
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2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH
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2
×
R'-SH
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+
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ROOH
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=
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R'-S-S-R'
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+
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H(2)O
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+
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ROH
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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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Biochem Biophys Res Commun
529:444-449
(2020)
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PubMed id:
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Crystal structure of the AhpD-like protein DR1765 from Deinococcus radiodurans R1.
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L.Zhao,
S.Jeong,
J.Zhang,
J.H.Jung,
J.I.Choi,
S.Lim,
M.K.Kim.
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ABSTRACT
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Deinococcus radiodurans is well known for its extreme resistance to ionizing
radiation (IR). Since reactive oxygen species generated by IR can damage various
cellular components, D. radiodurans has developed effective antioxidant systems
to cope with this oxidative stress. dr1765 from D. radiodurans is predicted to
encode an alkyl hydroperoxidase-like protein (AhpD family), which is implicated
in the reduction of hydrogen peroxide (H2O2) and organic
hydroperoxides. In this study, we constructed a dr1765 mutant strain (Δdr1765)
and examined the survival rate after H2O2 treatment.
Δdr1765 showed a significant decrease in the H2O2
resistance compared to the wild-type strain. We also determined the crystal
structure of DR1765 at 2.27 Å resolution. DR1765 adopted an all alpha helix
protein fold representative of the AhpD-like superfamily. Structural comparisons
of DR1765 with its structural homologues revealed that DR1765 possesses the
Glu74-Cys86-Tyr88-Cys89-His93 signature motif, which is conserved in the proton
relay system of AhpD. Complementation of Δdr1765 with dr1765 encoding C86A or
C89A mutation failed to restore the survival rate to wild-type level. Taken
together, these results suggest that DR1765 might function as an AhpD to protect
cells from oxidative stress.
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