PDBsum entry 2cdc

Oxidoreductase

PDB id: 2cdc

Contents

Protein chains

359 a.a. *

Ligands

NAP ×4

XYS-XYP ×2

XYS ×4

EDO ×3

XYP ×2

Metals

_ZN ×8

Waters ×1580

* Residue conservation analysis

PDB id:

2cdc

Name:

Oxidoreductase

Title:

Sulfolobus solfataricus glucose dehydrogenase 1 in complex with NADP and xylose

Structure:

Glucose dehydrogenase glucose 1-dehydrogenase, dhg-1. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Sulfolobus solfataricus. Organism_taxid: 2287. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.50Å R-factor: 0.206 R-free: 0.239

Authors:

C.C.Milburn,H.J.Lamble,A.Theodossis,D.W.Hough,M.J.Danson,G.L.Taylor

Key ref:

C.C.Milburn et al. (2006). The structural basis of substrate promiscuity in glucose dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus. J Biol Chem, 281, 14796-14804. PubMed id: 16556607 DOI: 10.1074/jbc.M601334200

Date:

23-Jan-06 Release date: 22-Mar-06

Protein chains

O93715  (GLCDH_SACSO) -  Glucose 1-dehydrogenase from Saccharolobus solfataricus

Seq: 366 a.a.

Struc: 359 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 1: E.C.1.1.1.120 - galactose 1-dehydrogenase (NADP(+)).
• Reaction: D-galactose + NADP⁺ = D-galactono-1,5-lactone + NADPH + H⁺

D-galactose (Bound ligand (Het Group name = XYS) matches with 83.33% similarity) + NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) = D-galactono-1,5-lactone + NADPH + H(+)

• Enzyme class 2: E.C.1.1.1.359 - aldose 1-dehydrogenase [NAD(P)(+)].
• Reaction:
  1. an aldopyranose + NADP⁺ = aldono-1,5-lactone + NADPH + H⁺
  2. an aldopyranose + NAD⁺ = aldono-1,5-lactone + NADH + H⁺

aldopyranose + NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) = aldono-1,5-lactone + NADPH + H(+)

aldopyranose + NAD(+) (Bound ligand (Het Group name = NAP) matches with 91.67% similarity) = aldono-1,5-lactone + NADH + H(+)

• Enzyme class 3: E.C.1.1.1.47 - glucose 1-dehydrogenase [NAD(P)(+)].
• Reaction:
  1. D-glucose + NADP⁺ = D-glucono-1,5-lactone + NADPH + H⁺
  2. D-glucose + NAD⁺ = D-glucono-1,5-lactone + NADH + H⁺

D-glucose (Bound ligand (Het Group name = XYS) matches with 83.33% similarity) + NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) = D-glucono-1,5-lactone + NADPH + H(+)

D-glucose (Bound ligand (Het Group name = XYS) matches with 83.33% similarity) + NAD(+) (Bound ligand (Het Group name = NAP) matches with 91.67% similarity) = D-glucono-1,5-lactone + NADH + H(+)

• Enzyme class 4: E.C.1.1.1.48 - D-galactose 1-dehydrogenase.
• Reaction: D-galactose + NAD⁺ = D-galactono-1,4-lactone + NADH + H⁺

D-galactose (Bound ligand (Het Group name = XYS) matches with 83.33% similarity) + NAD(+) (Bound ligand (Het Group name = NAP) matches with 91.67% similarity) = D-galactono-1,4-lactone + NADH + H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1074/jbc.M601334200

J Biol Chem 281:14796-14804 (2006)

PubMed id: 16556607

The structural basis of substrate promiscuity in glucose dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus.

C.C.Milburn, H.J.Lamble, A.Theodossis, S.D.Bull, D.W.Hough, M.J.Danson, G.L.Taylor.

ABSTRACT

The hyperthermophilic archaeon Sulfolobus solfataricus grows optimally above 80 degrees C and utilizes an unusual, promiscuous, non-phosphorylative Entner-Doudoroff pathway to metabolize both glucose and galactose. The first enzyme in this pathway, glucose dehydrogenase, catalyzes the oxidation of glucose to gluconate, but has been shown to have activity with a broad range of sugar substrates, including glucose, galactose, xylose, and L-arabinose, with a requirement for the glucose stereo configuration at the C2 and C3 positions. Here we report the crystal structure of the apo form of glucose dehydrogenase to a resolution of 1.8 A and a complex with its required cofactor, NADP+, to a resolution of 2.3 A. A T41A mutation was engineered to enable the trapping of substrate in the crystal. Complexes of the enzyme with D-glucose and D-xylose are presented to resolutions of 1.6 and 1.5 A, respectively, that provide evidence of selectivity for the beta-anomeric, pyranose form of the substrate, and indicate that this is the productive substrate form. The nature of the promiscuity of glucose dehydrogenase is also elucidated, and a physiological role for this enzyme in xylose metabolism is suggested. Finally, the structure suggests that the mechanism of sugar oxidation by this enzyme may be similar to that described for human sorbitol dehydrogenase.

Selected figure(s)

Figure 1.
FIGURE 1. Stereo images of the apo SsGDH tetramer (A) and monomer (B). The A-monomer is shown with the nucleotide-binding domain in red and the catalytic domain in blue. The position of the GXGXXG motif is highlighted in yellow. Zinc ions are shown as magenta spheres, and the catalytic zinc-coordinated water is shown as a green sphere.In B, the N and C termini of the monomer are indicated by green and red spheres, respectively.

Figure 3.
FIGURE 3. A, glucose bound to the SsGDH active site in the A-monomer. Coloring is as in Fig. 2B with the mutation T41A highlighted by orange carbons and the glucose molecule shown with purple carbons and red oxygens, with both C6-hydroxyl conformations. Unbiased F[c] -F[c] electron density for the substrate is shown as green mesh (contoured at 2.25 ). Hydrogen bonds between the protein and glucose are shown as broken black lines, and gray broken lines indicate interactions of 3.5-3.7 Å that are possible hydrogen bonds at the moment of catalysis. Asp^154 sits below the sugar ring interacting with the C2- and C3-hydroxyls. B, xylose bound to the SsGDH active site of monomer A. Coloring is as in A, but the glucose molecule is shown in the equatorial -form with purple carbons and red oxygens, and in the axial ( -form) with wheat-colored carbons. Unbiased F[c] - F[c] electron density for the substrate is shown as green mesh (contoured at 2.25 ). Hydrogen bonds between the protein and -xylose are shown as broken black lines, and gray broken lines indicate interactions of <3.5-3.7 Å that are possible hydrogen bonds at the moment of catalysis. Hydrogen bonds to the -form are not shown, because most, with the exception of the C1-OH interactions, are maintained and no new hydrogen bonds are formed in the -form. C, superposition of glucose (green) and xylose (blue) in the active site of the A-monomer. The two positions for O6 of glucose are displayed, as are the two positions of O1 of xylose. Glu^114 undergoes a conformational change between the glucose and xylose complex structures; the alternative position for this residue in the xylose structure is depicted in wheat-colored carbons.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 14796-14804) copyright 2006.

Figures were selected by an automated process.