PDBsum entry 6exf

Oxidoreductase

PDB id: 6exf

Contents

Protein chains

343 a.a.

315 a.a.

Ligands

LYS ×5

GOL ×2

Metals

_FE ×4

Waters ×805

PDB id:

6exf

Name:

Oxidoreductase

Title:

Crystal structure of the complex fe(ii)/alpha-ketoglutarate dependent dioxygenase kdo5 with fe(ii)/lysine

Structure:

L-lysine 4-hydroxylase. Chain: a, b, c, d. Synonym: alpha-ketoglutarate-dependent dioxygenase,kdo5,l-lysine hydroxylase. Engineered: yes

Source:

Flavobacterium sp.. Organism_taxid: 239. Gene: pmi10_03368. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.95Å R-factor: 0.179 R-free: 0.213

Authors:

T.Isabet,E.Stura,P.Legrand,A.Zaparucha,K.Bastard

Key ref:

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: 30410048

Date:

08-Nov-17 Release date: 14-Nov-18

Protein chains

J3BZS6  (LYS4O_FLASC) -  L-lysine 4-hydroxylase from Flavobacterium sp. (strain CF136)

Seq: 372 a.a.

Struc: 343 a.a.

Protein chain

J3BZS6  (LYS4O_FLASC) -  L-lysine 4-hydroxylase from Flavobacterium sp. (strain CF136)

Seq: 372 a.a.

Struc: 315 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.1.14.11.- - ?????

Sci Rep 8:16587 (2018)

PubMed id: 30410048

Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family.

K.Bastard, T.Isabet, E.A.Stura, P.Legrand, A.Zaparucha.

ABSTRACT

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.