PDBsum entry: 1txg

Oxidoreductase

PDB id: 1txg

Contents

Protein chains

335 a.a. *

Ligands

SO4 ×8

GOL ×2

NH4

Waters ×753

* Residue conservation analysis

PDB id:

1txg

Name:

Oxidoreductase

Title:

Structure of glycerol-3-phosphate dehydrogenase from archaeo fulgidus

Structure:

Glycerol-3-phosphate dehydrogenase [nad(p)+]. Chain: a, b. Synonym: NADP, h-dependent glycerol-3-phosphate dehydrogena engineered: yes

Source:

Archaeoglobus fulgidus. Organism_taxid: 2234. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.70Å R-factor: 0.151 R-free: 0.194

Authors:

S.Sakasegawa,C.H.Hagemeier,R.K.Thauer,L.O.Essen,S.Shima

Key ref:

S.Sakasegawa et al. (2004). Structural and functional analysis of the gpsA gene product of Archaeoglobus fulgidus: a glycerol-3-phosphate dehydrogenase with an unusual NADP+ preference. Protein Sci, 13, 3161-3171. PubMed id: 15557260 DOI: 10.1110/ps.04980304

Date:

05-Jul-04 Release date: 07-Dec-04

Protein chains

O29390  (GPDA_ARCFU) -  Glycerol-3-phosphate dehydrogenase [NAD(P)+]

Seq: 335 a.a.

Struc: 335 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.94 - Glycerol-3-phosphate dehydrogenase (NAD(P)(+)).
• Reaction: sn-glycerol 3-phosphate + NAD(P)(+) = glycerone phosphate + NAD(P)H

sn-glycerol 3-phosphate (Bound ligand (Het Group name = GOL) matches with 60.00% similarity) + NAD(P)(+) = glycerone phosphate + NAD(P)H

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (2 terms)
• Biological process: oxidation-reduction process (5 terms)
• Biochemical function: nucleotide binding (8 terms)

reference

DOI no: 10.1110/ps.04980304

Protein Sci 13:3161-3171 (2004)

PubMed id: 15557260

Structural and functional analysis of the gpsA gene product of Archaeoglobus fulgidus: a glycerol-3-phosphate dehydrogenase with an unusual NADP+ preference.

S.Sakasegawa, C.H.Hagemeier, R.K.Thauer, L.O.Essen, S.Shima.

ABSTRACT

NAD(+)-dependent glycerol-3-phosphate dehydrogenase (G3PDH) is generally absent in archaea, because archaea, unlike eukaryotes and eubacteria, utilize glycerol-1-phosphate instead of glycerol-3-phosphate for the biosynthesis of membrane lipids. Surprisingly, the genome of the hyperthermophilic archaeon Archaeoglobus fulgidus comprises a G3PDH ortholog, gpsA, most likely due to horizontal gene transfer from a eubacterial organism. Biochemical characterization proved G3PDH-like activity of the recombinant gpsA gene product. However, unlike other G3PDHs, the up to 85 degrees C thermostable A. fulgidus G3PDH exerted a 15-fold preference for NADPH over NADH. The A. fulgidus G3PDH bears the hallmarks of adaptation to halotolerance and thermophilicity, because its 1.7-A crystal structure showed a high surface density for negative charges and 10 additional intramolecular salt bridges compared to a mesophilic G3PDH structure. Whereas all amino acid residues required for dihydroxyacetone phosphate binding and reductive catalysis are highly conserved, the binding site for the adenine moiety of the NAD(P) cosubstrate shows a structural variation that reflects the observed NADPH preference, for example, by a putative salt bridge between R49 and the 2'-phosphate.

Selected figure(s)

Figure 4.
Figure 4. Structure of NADP+-dependent G3PDH from A. fulgidus. (A) Ribbon diagram of the G3PDH dimer when viewed perpendicular to the twofold noncrystallographic axis. One monomer is colored in green, one in blue. The N-terminal dinucleotide binding domains are shown in light green and in light blue; the C-terminal helix domains are shown in dark green and dark blue. The figure was produced with MOLSCRIPT (Kraulis 1991) and Raster3D (Merritt and Murphy 1994). (B) Fold topology diagram of the G3PDH monomer.

Figure 6.
Figure 6. Superposition (A) of the NADP+-dependent G3PDH monomer from A. fulgidus (blue) and of the G3PDH monomer from L. mexicana (green). The overall r.m.s.d. value between these models was 2.0 Å for 314 structurally equivalent residues. The loop between the indicated -helices 14 and 15 is visible in the structure of G3PDH from A. fulgidus but is disordered in the structure of G3PDH from L. mexicana, the only other structurally solved G3PDH (Suresh et al. 2000), if the substrate binding site is not fully occupied. The substrates NADPH and dihydroxyacetone phosphate were modeled into the structure of the A. fulgidus G3PDH at the corresponding binding sites known from the L. mexicana G3PDH structure (Choe et al. 2003). The structures of the L. mexicana enzyme and of the enzyme substrate complex were taken from the RCSB Protein Data Bank (accession codes 1N1E [PDB] and 1EVY [PDB] ). (B) Active site region of A. fulgidus G3PDH showing the predicted binding modes of the substrates glycerol-3-phosphate and NADP+. The substrate molecules were modeled into the structure using the SCULPT option of the program PyMOL, which permits interactive energy minimization.

The above figures are reprinted by permission from the Protein Society: Protein Sci (2004, 13, 3161-3171) copyright 2004.

Figures were selected by the author.