PDBsum entry 1hye

Oxidoreductase

PDB id: 1hye

Contents

Protein chain

307 a.a. *

Ligands

NAP

Waters ×75

* Residue conservation analysis

PDB id:

1hye

Name:

Oxidoreductase

Title:

Crystal structure of the mj0490 gene product, the family of lactate/malate dehydrogenase, dimeric structure

Structure:

L-lactate/malate dehydrogenase. Chain: a. Engineered: yes

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: mj0490. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.90Å R-factor: 0.194 R-free: 0.228

Authors:

B.I.Lee,C.Chang,S.-J.Cho,S.W.Suh

Key ref:

B.I.Lee et al. (2001). Crystal structure of the MJ0490 gene product of the hyperthermophilic archaebacterium Methanococcus jannaschii, a novel member of the lactate/malate family of dehydrogenases. J Mol Biol, 307, 1351-1362. PubMed id: 11292347 DOI: 10.1006/jmbi.2001.4532

Date:

19-Jan-01 Release date: 18-Apr-01

Protein chain

Q60176  (MDH_METJA) -  L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 313 a.a.

Struc: 307 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.375 - L-2-hydroxycarboxylate dehydrogenase [NAD(P)(+)].
• Reaction:
  1. a (2S)-2-hydroxycarboxylate + NAD⁺ = a 2-oxocarboxylate + NADH + H⁺
  2. a (2S)-2-hydroxycarboxylate + NADP⁺ = a 2-oxocarboxylate + NADPH + H⁺

(2S)-2-hydroxycarboxylate + NAD(+) (Bound ligand (Het Group name = NAP) matches with 91.67% similarity) = 2-oxocarboxylate + NADH + H(+)

(2S)-2-hydroxycarboxylate + NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) = 2-oxocarboxylate + NADPH + H(+)

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

reference

DOI no: 10.1006/jmbi.2001.4532

J Mol Biol 307:1351-1362 (2001)

PubMed id: 11292347

Crystal structure of the MJ0490 gene product of the hyperthermophilic archaebacterium Methanococcus jannaschii, a novel member of the lactate/malate family of dehydrogenases.

B.I.Lee, C.Chang, S.J.Cho, S.H.Eom, K.K.Kim, Y.G.Yu, S.W.Suh.

ABSTRACT

The MJ0490 gene, one of the only two genes of Methanococcus jannaschii showing sequence similarity to the lactate/malate family of dehydrogenases, was classified initially as coding for a putative l-lactate dehydrogenase (LDH). It has been re-classified as a malate dehydrogenase (MDH) gene, because it shows significant sequence similarity to MT0188, MDH II from Methanobacterium thermoautotrophicum strain DeltaH. The three-dimensional structure of its gene product has been determined in two crystal forms: a "dimeric" structure in the orthorhombic crystal at 1.9 A resolution and a "tetrameric" structure in the tetragonal crystal at 2.8 A. These structures share a similar subunit fold with other LDHs and MDHs. The tetrameric structure resembles typical tetrameric LDHs. The dimeric structure is equivalent to the P-dimer of tetrameric LDHs, unlike dimeric MDHs, which correspond to the Q-dimer. The structure reveals that the cofactor NADP(H) is bound at the active site, despite the fact that it was not intentionally added during protein purification and crystallization. The preference of NADP(H) over NAD(H) has been supported by activity assays. The cofactor preference is explained by the presence of a glycine residue in the cofactor binding pocket (Gly33), which replaces a conserved aspartate (or glutamate) residue in other NAD-dependent LDHs or MDHs. Preference for NADP(H) is contributed by hydrogen bonds between the oxygen atoms of the monophosphate group and the ribose sugar of adenosine in NADP(H) and the side-chains of Ser9, Arg34, His36, and Ser37. The MDH activity of MJ0490 is made possible by Arg86, which is conserved in MDHs but not in LDHs. The enzymatic assay showed that the MJ0490 protein possesses the fructose-1,6-bisphosphate-activated LDH activity (reduction). Thus the MJ0490 gene product appears to be a novel member of the lactate/malate dehydrogenase family, displaying an LDH scaffold and exhibiting a relaxed substrate and cofactor specificities in NADP(H) and NAD(H)-dependent malate and lactate dehydrogenase reactions.

Selected figure(s)

Figure 2.
Figure 2. Overall structure of MJ0490 protein. (a) Stereo ribbon diagram of the subunit model, and stereo C^a tracings of (b) terameric structure and (c) dimeric structure. NADP+ molecules are shown in orange (in (a)) or in blue (in (b), and (c)). These Figures were drawn by MOLSCRIPT [Kraulis 1991] and Raster3D [Merritt and Murphy 1994].

Figure 3.
Figure 3. (a) Stereo view of the final (2F[o] - F[c]) electron density map around the bound NADP+, calculated using 20.0-1.9 Å data and contoured at 1.0s. (b) Stereo view of the cofactor binding site. The NADP+ molecule is in dark olive green and interacting residues are drawn in orange. Broken lines indicate hydrogen bonds or close contacts.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 307, 1351-1362) copyright 2001.

Figures were selected by an automated process.