PDBsum entry: 1lj8

Oxidoreductase

PDB id: 1lj8

Contents

Protein chain

492 a.a. *

Ligands

NAD

Waters ×437

* Residue conservation analysis

PDB id:

1lj8

Name:

Oxidoreductase

Title:

Crystal structure of mannitol dehydrogenase in complex with NAD

Structure:

Mannitol dehydrogenase. Chain: a. Engineered: yes

Source:

Pseudomonas fluorescens. Organism_taxid: 294. Strain: dsm50106. Gene: mtld. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.70Å R-factor: 0.171 R-free: 0.197

Authors:

K.L.Kavanagh,M.Klimacek,B.Nidetzky,D.K.Wilson

Key ref:

K.L.Kavanagh et al. (2002). Crystal structure of Pseudomonas fluorescens mannitol 2-dehydrogenase binary and ternary complexes. Specificity and catalytic mechanism. J Biol Chem, 277, 43433-43442. PubMed id: 12196534 DOI: 10.1074/jbc.M206914200

Date:

19-Apr-02 Release date: 15-Nov-02

Protein chain

O08355  (O08355_PSEFL) -  Mannitol dehydrogenase

Seq: 493 a.a.

Struc: 492 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.67 - Mannitol 2-dehydrogenase.
• Reaction: D-mannitol + NAD⁺ = D-fructose + NADH

D-mannitol + NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly) = D-fructose + NADH

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

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (8 terms)

reference

DOI no: 10.1074/jbc.M206914200

J Biol Chem 277:43433-43442 (2002)

PubMed id: 12196534

Crystal structure of Pseudomonas fluorescens mannitol 2-dehydrogenase binary and ternary complexes. Specificity and catalytic mechanism.

K.L.Kavanagh, M.Klimacek, B.Nidetzky, D.K.Wilson.

ABSTRACT

Long-chain mannitol dehydrogenases are secondary alcohol dehydrogenases that are of wide interest because of their involvement in metabolism and potential applications in agriculture, medicine, and industry. They differ from other alcohol and polyol dehydrogenases because they do not contain a conserved tyrosine and are not dependent on Zn(2+) or other metal cofactors. The structures of the long-chain mannitol 2-dehydrogenase (54 kDa) from Pseudomonas fluorescens in a binary complex with NAD(+) and ternary complex with NAD(+) and d-mannitol have been determined to resolutions of 1.7 and 1.8 A and R-factors of 0.171 and 0.176, respectively. These results show an N-terminal domain that includes a typical Rossmann fold. The C-terminal domain is primarily alpha-helical and mediates mannitol binding. The electron lone pair of Lys-295 is steered by hydrogen-bonding interactions with the amide oxygen of Asn-300 and the main-chain carbonyl oxygen of Val-229 to act as the general base. Asn-191 and Asn-300 are involved in a web of hydrogen bonding, which precisely orients the mannitol O2 proton for abstraction. These residues also aid in stabilizing a negative charge in the intermediate state and in preventing the formation of nonproductive complexes with the substrate. The catalytic lysine may be returned to its unprotonated state using a rectifying proton tunnel driven by Glu-292 oscillating among different environments. Despite low sequence homology, the closest structural neighbors are glycerol-3-phosphate dehydrogenase, N-(1-d-carboxylethyl)-l-norvaline dehydrogenase, UDP-glucose dehydrogenase, and 6-phosphogluconate dehydrogenase, indicating a possible evolutionary relationship among these enzymes.

Selected figure(s)

Figure 2.
Fig. 2. Schematic diagram of MDH secondary structure. -Strands are colored blue and numbered 1- 16; strands within the canonical dinucleotide binding motif are also labeled sequentially as A-F. -Helices are colored green and numbered 1-20.

Figure 5.
Fig. 5. A, overlay of the binary and ternary complexes of pfMDH showing substrates NAD and mannitol with Lys-295 and mechanistically important interactions. The binary complex is gray, and in the ternary complex, residues from the N-terminal domain are colored red, those from the C-terminal domain are colored green, and waters are colored gold. Selected hydrogen bonds are drawn for each complex, and an arrow shows the rotation of the side chain of Glu-292 toward bulk solvent (see "Results and Discussion"). B, a proposed high pH reaction mechanism based upon the structure of the enzyme.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 43433-43442) copyright 2002.

Figures were selected by an automated process.