PDBsum entry 2vbg

Lyase

PDB id: 2vbg

Contents

Protein chains

546 a.a. *

Ligands

R1T ×2

Metals

_MG ×2

Waters ×950

* Residue conservation analysis

PDB id:

2vbg

Name:

Lyase

Title:

The complex structure of the branched-chain keto acid decarboxylase (kdca) from lactococcus lactis with 2r-1-hydroxyethyl-deazathdp

Structure:

Branched-chain alpha-ketoacid decarboxylase. Chain: a, b. Synonym: branched-chain keto acid decarboxylase. Engineered: yes. Other_details: chain a and b contain the complete enzyme sequence and short n-terminal tags with linkers, which are bound in adjacent dimers in the crystal.

Source:

Lactococcus lactis. Organism_taxid: 1358. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.80Å R-factor: 0.165 R-free: 0.205

Authors:

C.L.Berthold,D.Gocke,M.D.Wood,F.Leeper,M.Pohl,G.Schneider

Key ref:

C.L.Berthold et al. (2007). Structure of the branched-chain keto acid decarboxylase (KdcA) from Lactococcus lactis provides insights into the structural basis for the chemoselective and enantioselective carboligation reaction. Acta Crystallogr D Biol Crystallogr, 63, 1217-1224. PubMed id: 18084069 DOI: 10.1107/S0907444907050433

Date:

12-Sep-07 Release date: 27-Nov-07

Protein chains

Q6QBS4  (Q6QBS4_9LACT) -  Branched-chain alpha-ketoacid decarboxylase from Lactococcus lactis

Seq: 547 a.a.

Struc: 546 a.a.

DOI no: 10.1107/S0907444907050433

Acta Crystallogr D Biol Crystallogr 63:1217-1224 (2007)

PubMed id: 18084069

Structure of the branched-chain keto acid decarboxylase (KdcA) from Lactococcus lactis provides insights into the structural basis for the chemoselective and enantioselective carboligation reaction.

C.L.Berthold, D.Gocke, M.D.Wood, F.J.Leeper, M.Pohl, G.Schneider.

ABSTRACT

The thiamin diphosphate (ThDP) dependent branched-chain keto acid decarboxylase (KdcA) from Lactococcus lactis catalyzes the decarboxylation of 3-methyl-2-oxobutanoic acid to 3-methylpropanal (isobutyraldehyde) and CO2. The enzyme is also able to catalyze carboligation reactions with an exceptionally broad substrate range, a feature that makes KdcA a potentially valuable biocatalyst for C-C bond formation, in particular for the enzymatic synthesis of diversely substituted 2-hydroxyketones with high enantioselectivity. The crystal structures of recombinant holo-KdcA and of a complex with an inhibitory ThDP analogue mimicking a reaction intermediate have been determined to resolutions of 1.6 and 1.8 A, respectively. KdcA shows the fold and cofactor-protein interactions typical of thiamin-dependent enzymes. In contrast to the tetrameric assembly displayed by most other ThDP-dependent decarboxylases of known structure, KdcA is a homodimer. The crystal structures provide insights into the structural basis of substrate selectivity and stereoselectivity of the enzyme and thus are suitable as a framework for the redesign of the substrate profile in carboligation reactions.

Selected figure(s)

Figure 2.
Figure 2 A schematic representation of the S-pocket. (a) When there is no S-pocket or an S-pocket that is too small to fit the acceptor substrate side chain R, it will bind with the Si face towards the enamine and the (R)-enantiomer will be formed. (b) Perfect fit of the acceptor substrate side chain in the S-pocket above the thiazolium ring will allow the substrate to align, resulting in the (S)-enantiomer.

Figure 8.
Figure 8 Benzaldehyde modelled as acyl donor aldehyde covalently bound to ThDP in the form of the enamine (grey) and as acceptor substrate (blue) with the Si side facing the enamine.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 1217-1224) copyright 2007.

Figures were selected by an automated process.