PDBsum entry 2v6b

Oxidoreductase

PDB id: 2v6b

Contents

Protein chains

274 a.a. *

Waters ×121

* Residue conservation analysis

PDB id:

2v6b

Name:

Oxidoreductase

Title:

Crystal structure of lactate dehydrogenase from deinococcus radiodurans (apo form)

Structure:

L-lactate dehydrogenase. Chain: a, b, c, d. Synonym: l-ldh. Engineered: yes

Source:

Deinococcus radiodurans. Organism_taxid: 1299. Expressed in: escherichia coli dh5[alpha]. Expression_system_taxid: 668369.

Resolution:

2.50Å R-factor: 0.230 R-free: 0.250

Authors:

N.Coquelle,E.Fioravanti,M.Weik,F.Vellieux

Key ref:

N.Coquelle et al. (2007). Activity, stability and structural studies of lactate dehydrogenases adapted to extreme thermal environments. J Mol Biol, 374, 547-562. PubMed id: 17936781 DOI: 10.1016/j.jmb.2007.09.049

Date:

16-Jul-07 Release date: 25-Sep-07

Protein chains

P50933  (LDH_DEIRA) -  L-lactate dehydrogenase from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 304 a.a.

Struc: 274 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.27 - L-lactate dehydrogenase.
• Reaction: (S)-lactate + NAD⁺ = pyruvate + NADH + H⁺

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

reference

DOI no: 10.1016/j.jmb.2007.09.049

J Mol Biol 374:547-562 (2007)

PubMed id: 17936781

Activity, stability and structural studies of lactate dehydrogenases adapted to extreme thermal environments.

N.Coquelle, E.Fioravanti, M.Weik, F.Vellieux, D.Madern.

ABSTRACT

Lactate dehydrogenase (LDH) catalyzes the conversion of pyruvate to lactate with concomitant oxidation of NADH during the last step in anaerobic glycolysis. In the present study, we present a comparative biochemical and structural analysis of various LDHs adapted to function over a large temperature range. The enzymes were from Champsocephalus gunnari (an Antarctic fish), Deinococcus radiodurans (a mesophilic bacterium) and Thermus thermophilus (a hyperthermophilic bacterium). The thermodynamic activation parameters of these LDHs indicated that temperature adaptation from hot to cold conditions was due to a decrease in the activation enthalpy and an increase in activation entropy. The crystal structures of these LDHs have been solved. Pairwise comparisons at the structural level, between hyperthermophilic versus mesophilic LDHs and mesophilic versus psychrophilic LDHs, have revealed that temperature adaptation is due to a few amino acid substitutions that are localized in critical regions of the enzyme. These substitutions, each having accumulating effects, play a role in either the conformational stability or the local flexibility or in both. Going from hot- to cold-adapted LDHs, the various substitutions have decreased the number of ion pairs, reduced the size of ionic networks, created unfavorable interactions involving charged residues and induced strong local disorder. The analysis of the LDHs adapted to extreme temperatures shed light on how evolutionary processes shift the subtle balance between overall stability and flexibility of an enzyme.

Selected figure(s)

Figure 2.
Fig. 2. Ribbon diagram of the apo form of tetrameric TtLDH. The four monomers are labeled A–D.

Figure 3.
Fig. 3. A 30 Å slice through a ribbon diagram of a monomer of TtLDH complexed with oxamate and NADH. The color scheme used is related to C^α deviation between the apo and ternary complex. The rainbow scale bar illustrates values of deviation in angstroms. Inset: RMSD between C^α atoms in the superimposed subunits of TtLDH (apo versus ternary complex). The mobile regions (MR) that display the largest deviations are indicated.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 374, 547-562) copyright 2007.

Figures were selected by an automated process.