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PDBsum entry 6f2e
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Oxidoreductase
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PDB id
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6f2e
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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 apo fe(ii)/alpha-ketoglutarate dependent dioxygenase kdo1
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Structure:
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L-lysine 3-hydroxylase. Chain: a, b, c, d. Synonym: alpha-ketoglutarate-dependent dioxygenase,kdo1,l-lysine hydroxylase. Engineered: yes
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Source:
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Catenulispora acidiphila (strain dsm 44928 / nrrl b-24433 / nbrc 102108 / jcm 14897). Organism_taxid: 479433. Gene: caci_0231. Expressed in: escherichia coli. Expression_system_taxid: 562
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Resolution:
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1.90Å
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R-factor:
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0.178
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R-free:
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0.203
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Authors:
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T.Isabet,E.A.Stura,P.Legrand,A.Zaparucha,K.Bastard
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Key ref:
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K.Bastard
et al.
(2018).
Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family.
Sci Rep,
8,
16587.
PubMed id:
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Date:
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24-Nov-17
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Release date:
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14-Nov-18
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PROCHECK
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Headers
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References
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C7QJ42
(LYS3O_CATAD) -
L-lysine 3-hydroxylase from Catenulispora acidiphila (strain DSM 44928 / JCM 14897 / NBRC 102108 / NRRL B-24433 / ID139908)
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Seq:
Struc:
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358 a.a.
329 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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Sci Rep
8:16587
(2018)
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PubMed id:
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Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family.
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K.Bastard,
T.Isabet,
E.A.Stura,
P.Legrand,
A.Zaparucha.
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ABSTRACT
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Iron(II)/α-ketoacid-dependent oxygenases (αKAOs) are enzymes that catalyze the
oxidation of unactivated C-H bonds, mainly through hydroxylation. Among these,
those that are active towards amino-acids and their derivatives are grouped in
the Clavaminate Synthase Like (CSL) family. CSL enzymes exhibit high regio- and
stereoselectivities with strict substrate specificity. This study reports the
structural elucidation of two new regiodivergent members, KDO1 and KDO5, active
towards lysine, and the structural and computational analysis of the whole
family through modelling and classification of active sites. The structures of
KDO1 and KDO5 in complex with their ligands show that one exact position in the
active site controls the regioselectivity of the reaction. Our results suggest
that the substrate specificity and high stereoselectivity typical of this family
is linked to a lid that closes up in order to form a sub-pocket around the side
chain of the substrate. This dynamic lid is found throughout the family with
varying sequence and length and is associated with a conserved stable dimeric
interface. Results from this study could be a starting-point for exploring the
functional diversity of the CSL family and direct in vitro screening in the
search for new enzymatic activities.
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