PDBsum entry 2r4j

Oxidoreductase

PDB id: 2r4j

Contents

Protein chains

494 a.a. *

Ligands

BOG ×6

PO4 ×2

FAD ×2

EDO ×26

IMD ×6

13P ×2

BCN ×3

TAM

Waters ×277

* Residue conservation analysis

PDB id:

2r4j

Name:

Oxidoreductase

Title:

Crystal structure of escherichia coli semet substituted glycerol-3- phosphate dehydrogenase in complex with dhap

Structure:

Aerobic glycerol-3-phosphate dehydrogenase. Chain: a, b. Engineered: yes

Source:

Escherichia coli. Gene: glpd, glyd. Expressed in: escherichia coli

Resolution:

1.96Å R-factor: 0.214 R-free: 0.263

Authors:

J.I.Yeh,S.Du,U.Chinte

Key ref:

J.I.Yeh et al. (2008). Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism. Proc Natl Acad Sci U S A, 105, 3280-3285. PubMed id: 18296637 DOI: 10.1073/pnas.0712331105

Date:

31-Aug-07 Release date: 03-Jun-08

Protein chains

P13035  (GLPD_ECOLI) -  Aerobic glycerol-3-phosphate dehydrogenase from Escherichia coli (strain K12)

Seq: 501 a.a.

Struc: 494 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.5.3 - glycerol-3-phosphate dehydrogenase.
• Reaction: a quinone + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + a quinol

quinone (Bound ligand (Het Group name = 13P) corresponds exactly) + sn-glycerol 3-phosphate (Bound ligand (Het Group name = BOG) matches with 40.00% similarity) = dihydroxyacetone phosphate + quinol

• Cofactor: Flavin

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

reference

DOI no: 10.1073/pnas.0712331105

Proc Natl Acad Sci U S A 105:3280-3285 (2008)

PubMed id: 18296637

Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.

J.I.Yeh, U.Chinte, S.Du.

ABSTRACT

Sn-glycerol-3-phosphate dehydrogenase (GlpD) is an essential membrane enzyme, functioning at the central junction of respiration, glycolysis, and phospholipid biosynthesis. Its critical role is indicated by the multitiered regulatory mechanisms that stringently controls its expression and function. Once expressed, GlpD activity is regulated through lipid-enzyme interactions in Escherichia coli. Here, we report seven previously undescribed structures of the fully active E. coli GlpD, up to 1.75 A resolution. In addition to elucidating the structure of the native enzyme, we have determined the structures of GlpD complexed with substrate analogues phosphoenolpyruvate, glyceric acid 2-phosphate, glyceraldehyde-3-phosphate, and product, dihydroxyacetone phosphate. These structural results reveal conformational states of the enzyme, delineating the residues involved in substrate binding and catalysis at the glycerol-3-phosphate site. Two probable mechanisms for catalyzing the dehydrogenation of glycerol-3-phosphate are envisioned, based on the conformational states of the complexes. To further correlate catalytic dehydrogenation to respiration, we have additionally determined the structures of GlpD bound with ubiquinone analogues menadione and 2-n-heptyl-4-hydroxyquinoline N-oxide, identifying a hydrophobic plateau that is likely the ubiquinone-binding site. These structures illuminate probable mechanisms of catalysis and suggest how GlpD shuttles electrons into the respiratory pathway. Glycerol metabolism has been implicated in insulin signaling and perturbations in glycerol uptake and catabolism are linked to obesity in humans. Homologs of GlpD are found in practically all organisms, from prokaryotes to humans, with >45% consensus protein sequences, signifying that these structural results on the prokaryotic enzyme may be readily applied to the eukaryotic GlpD enzymes.

Selected figure(s)

Figure 1.
Schematic of the glycerol metabolic pathway in E. coli. Protein members of the glycerol metabolic pathway includes glycerol facilitator (GlpF/AQP), a member of the aquaporin family of major intrinsic proteins. The soluble glycerol kinase (GK) phosphorylates glycerol to G3P. Another membrane protein constituent of this pathway is the transporter for the uptake of G3P (GlpT) with concomitant exit of Pi. Oxidation of G3P to DHAP is catalyzed by the monotopic membrane enzyme, glycerol-3-phosphate dehydrogenase (GlpD), a primary dehydrogenase. Concurrent with oxidation of G3P is reduction of flavin adenine dinucleotide (FAD) to FADH[2], which passes on electrons to ubiquinone (UQ) forming the reduced form (UQH[2]) and ultimately shuttling electrons to oxygen or nitrate.

Figure 4.
Reaction scheme. Schematic diagram showing the active site with G3P, modeled from the GAP-complex structure. Only selected interactions in the active site are shown. Dotted lines indicate distances, in angstroms, between atoms in proximity for hydrogen bonding interactions. For FAD, only the isoalloxazine ring is depicted.

Figures were selected by an automated process.