PDBsum entry 2a8x

Oxidoreductase

PDB id: 2a8x

Contents

Protein chains

464 a.a. *

Ligands

FAD ×2

MPD

Waters ×333

* Residue conservation analysis

PDB id:

2a8x

Name:

Oxidoreductase

Title:

Crystal structure of lipoamide dehydrogenase from mycobacterium tuberculosis

Structure:

Dihydrolipoyl dehydrogenase. Chain: a, b. Synonym: lipoamide dehydrogenase. E3 component of alpha keto acid dehydrogenase complexes. Dihydrolipoamide dehydrogenase. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: rv0462, mt0478, lpdc. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.40Å R-factor: 0.199 R-free: 0.246

Authors:

K.R.Rajashankar,R.Bryk,R.Kniewel,J.A.Buglino,C.F.Nathan,C.D.Lima

Key ref:

K.R.Rajashankar et al. (2005). Crystal structure and functional analysis of lipoamide dehydrogenase from Mycobacterium tuberculosis. J Biol Chem, 280, 33977-33983. PubMed id: 16093239 DOI: 10.1074/jbc.M507466200

Date:

10-Jul-05 Release date: 16-Aug-05

Protein chains

P9WHH9  (DLDH_MYCTU) -  Dihydrolipoyl dehydrogenase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 464 a.a.

Struc: 464 a.a.

Enzyme reactions

• Enzyme class: E.C.1.8.1.4 - dihydrolipoyl dehydrogenase.
• Pathway: Glycine Cleavage System
• Reaction: N₆-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD⁺ = N₆-[(R)-lipoyl]- L-lysyl-[protein] + NADH + H⁺
• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M507466200

J Biol Chem 280:33977-33983 (2005)

PubMed id: 16093239

Crystal structure and functional analysis of lipoamide dehydrogenase from Mycobacterium tuberculosis.

K.R.Rajashankar, R.Bryk, R.Kniewel, J.A.Buglino, C.F.Nathan, C.D.Lima.

ABSTRACT

We report the 2.4 A crystal structure for lipoamide dehydrogenase encoded by lpdC from Mycobacterium tuberculosis. Based on the Lpd structure and sequence alignment between bacterial and eukaryotic Lpd sequences, we generated single point mutations in Lpd and assayed the resulting proteins for their ability to catalyze lipoamide reduction/oxidation alone and in complex with other proteins that participate in pyruvate dehydrogenase and peroxidase activities. The results suggest that amino acid residues conserved in mycobacterial species but not conserved in eukaryotic Lpd family members modulate either or both activities and include Arg-93, His-98, Lys-103, and His-386. In addition, Arg-93 and His-386 are involved in forming both "open" and "closed" active site conformations, suggesting that these residues play a role in dynamically regulating Lpd function. Taken together, these data suggest protein surfaces that should be considered while developing strategies for inhibiting this enzyme.

Selected figure(s)

Figure 1.
FIGURE 1. Structure of lipoamide dehydrogenase from M. tuberculosis. A, ribbon representation of LPD dimer. Protomers are colored blue or red. N and C demarcate the blue and red polypeptide termini, respectively. Residues (Cys-41, Cys-46, His-443', Glu-448') within the active sites are shown in stick representation. FAD and the active site are indicated by arrows and labeled. B, Stereo view and close-up of the active site with respective active site residues in A labeled with putative hydrogen bonds depicted as gray dashed lines. A simulated annealing "omit" map is shown contoured around the FAD cofactor at 1.0 . Structural representations prepared with PyMol unless otherwise indicated (34).

Figure 4.
FIGURE 4. Cross-sectional view of the LPD active site in two states. A, surface representation of Lpd illustrating both open and closed conformation of the active site. B, individual figures showing both open and closed states of the active site. Arg-93, His-386, FAD, Cys-41 and Cys-46 are shown in stick representation and labeled. Both MPD and FAD are indicated by labels. The purported binding site for NADH and the lipoylated DlaT side chain are indicated by arrows and labels in A.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 33977-33983) copyright 2005.

Figures were selected by the author.