PDBsum entry 1b8v

Oxidoreductase

PDB id: 1b8v

Contents

Protein chain

327 a.a. *

Ligands

NAD

Waters ×127

* Residue conservation analysis

PDB id:

1b8v

Name:

Oxidoreductase

Title:

Malate dehydrogenase from aquaspirillum arcticum

Structure:

Protein (malate dehydrogenase). Chain: a

Source:

Aquaspirillum arcticum. Organism_taxid: 87645

Biol. unit:

Dimer (from PDB file)

Resolution:

2.10Å R-factor: 0.183

Authors:

S.Y.Kim,K.Y.Hwang,S.H.Kim,Y.S.Han,Y.Cho

Key ref:

S.Y.Kim et al. (1999). Structural basis for cold adaptation. Sequence, biochemical properties, and crystal structure of malate dehydrogenase from a psychrophile Aquaspirillium arcticum. J Biol Chem, 274, 11761-11767. PubMed id: 10206992 DOI: 10.1074/jbc.274.17.11761

Date:

02-Feb-99 Release date: 09-Jul-99

Protein chain

Q9ZF99  (MDH_AQUAR) -  Malate dehydrogenase from Aquaspirillum arcticum

Seq: 329 a.a.

Struc: 327 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.37 - malate dehydrogenase.
• Pathway: Citric acid cycle
• Reaction: (S)-malate + NAD⁺ = oxaloacetate + NADH + H⁺

(S)-malate + NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly) = oxaloacetate + NADH + H(+)

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

reference

DOI no: 10.1074/jbc.274.17.11761

J Biol Chem 274:11761-11767 (1999)

PubMed id: 10206992

Structural basis for cold adaptation. Sequence, biochemical properties, and crystal structure of malate dehydrogenase from a psychrophile Aquaspirillium arcticum.

S.Y.Kim, K.Y.Hwang, S.H.Kim, H.C.Sung, Y.S.Han, Y.Cho.

ABSTRACT

Aquaspillium arcticum is a psychrophilic bacterium that was isolated from arctic sediment and grows optimally at 4 degrees C. We have cloned, purified, and characterized malate dehydrogenase from A. arcticum (Aa MDH). We also have determined the crystal structures of apo-Aa MDH, Aa MDH.NADH binary complex, and Aa MDH.NAD.oxaloacetate ternary complex at 1.9-, 2.1-, and 2.5-A resolutions, respectively. The Aa MDH sequence is most closely related to the sequence of a thermophilic MDH from Thermus flavus (Tf MDH), showing 61% sequence identity and over 90% sequence similarity. Stability studies show that Aa MDH has a half-life of 10 min at 55 degrees C, whereas Tf MDH is fully active at 90 degrees C for 1 h. Aa MDH shows 2-3-fold higher catalytic efficiency compared with a mesophilic or a thermophilic MDH at the temperature range 4-10 degrees C. Structural comparison of Aa MDH and Tf MDH suggests that the increased relative flexibility of active site residues, favorable surface charge distribution for substrate and cofactor, and the reduced intersubunit ion pair interactions may be the major factors for the efficient catalytic activity of Aa MDH at low temperatures.

Selected figure(s)

Figure 2.
Fig. 2. a, a simulated annealed omit map around the NADH in Aa MDH·NADH complex. The map is shown with a contour level of 1 . b, a stereodiagram of the NADH binding site in Aa MDH. Important residues interacting with NADH are labeled, and distances between them are shown.

Figure 3.
Fig. 3. a, an omit map around the oxaloacetate in the Aa MDH ternary complex. The map is shown with a contour level of 1 . b, a stereodiagram of the oxaloacetate binding site in Aa MDH. Important residues interacting with oxaloacetate are labeled, and distances between them are shown.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 11761-11767) copyright 1999.

Figures were selected by an automated process.