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

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 9, 2008, Pages 3280-3285

  Yeh, Joanne I ^a   Chinte, Unmesh ^a   Du, Shoucheng ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

Electron transfer; Glycerol metabolism; Glyceroneogenesis; Ubiquinone

Indexed keywords

2 HEPTYL 4 HYDROXYQUINOLINE 1 OXIDE; DIHYDROXYACETONE PHOSPHATE; GLYCERALDEHYDE 3 PHOSPHATE; GLYCERIC ACID 2 PHOSPHATE; GLYCEROL 3 PHOSPHATE DEHYDROGENASE; MENADIONE; PHOSPHATE; PHOSPHOENOLPYRUVATE; UBIQUINONE; BACTERIAL PROTEIN; GLYCEROL;

ALCOHOL METABOLISM; ARTICLE; BINDING SITE; BREATHING; CATALYSIS; COMPLEX FORMATION; CONTROLLED STUDY; DEHYDROGENATION; ENZYME CONFORMATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; ESCHERICHIA COLI; MOLECULAR DOCKING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; CELL RESPIRATION; CHEMISTRY; ELECTRON TRANSPORT; ENZYMOLOGY; METABOLISM; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

ESCHERICHIA COLI; EUKARYOTA; PROKARYOTA;

BACTERIAL PROTEINS; BINDING SITES; CATALYSIS; CELL RESPIRATION; CRYSTALLOGRAPHY, X-RAY; ELECTRON TRANSPORT; ESCHERICHIA COLI; GLYCEROL; GLYCEROLPHOSPHATE DEHYDROGENASE; PROTEIN CONFORMATION;

EID: 42149117451     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0712331105     Document Type: Article

References (46)

1. Austin D, Larson TJ (1991) Nucleotide sequence of the glpD gene encoding aerobic sn-glycerol 3-phosphate dehydrogenase of Escherichia coli K-12. J Bacteriol 173:101-107.
2. Beijer L, Nilsson R-P, Holmberg C, Rutberg L (1993) The glpP and glpF genes of the glycerol regulon in Bacillus subtilis. J Gen Microbiol 139:349-359.
3. Weissenborn DL, Wittekindt N, Larson TJ (1992) Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12. J Biol Chem 267:6122-6131.
4. Schryvers A, Lohmeier E, Weiner JE (1978) Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia coli. J Biol Chem 253:783-788.
5. Robinson JJ, Weiner JH (1980) The effect of amphipaths on the flavin-linked aerobic glycerol-3-phosphate dehydrogenase from Escherichia coli. Can J Biochem 48:1172-1178.
6. Weiner JH, Heppel LA (1972) Purification of the membrane-bound and pyridine nucleotide-independent L-glycerol 3-phosphate dehydrogenase from Escherichia coli. Biochem Biophys Res Commun 47:1360-1365.
7. Yankovskaya V, et al. (2003) Architecture of succinate dehydrogenase and reactive oxygen species generation. Science 299:700-704.
8. Battaile KP, et al. (2002) Crystal structure of rat short chain acyl-CoA dehydrogenase complexed with acetoacetyl-CoA: Comparison with other acyl-CoA dehydrogenases. J Biol Chem 277:12200-12207.
9. Sun F, et al. (2005) Crystal structure of mitochondrial respiratory membrane protein complex II. Cell 121:1043-1057.
10. Parsonage D, Luba J, Mallett TC, Claiborne, A (1998) The soluble α-glycerophosphate oxidase from Enterococcus casseliflavus. J Biol Chem 273:23812-23822.
11. Haddock BA, Jones CW (1977) Bacterial respiration. Bacteriol Rev 41:47-99.
12. Holm L, Sander C (1996) Mapping the protein universe. Science 273:595-603.
13. Pearl FM, et al. (2003) The CATH database: An extended protein family resource for structural and functional genomics. Nucleic Acids Res 31:452-455.
14. Garrib A, McMurray WC (1986) Purification and characterization of glycerol-3-phosphate dehydrogenase (flavin-linked) from rat liver mitochondria. J Biol Chem 261:8042-8048.
15. Cottingham IR, Ragan CI (1980) Purification and properties of L-3-glycerophosphate dehydrogenase from pig brain mitochondria. Biochem J 192:9-18.
16. Yeh JI, et al. (2004) Structures of enterococcal glycerol kinase in the absence and presence of glycerol: Correlation of conformation to substrate binding and a mechanism of activation by phosphorylation. Biochemistry 43:362-373.
17. Kogut M, Lightbown JW (1962) Selective inhibition by 2-heptyl-4- hydroxyquinoline N-oxide of certain oxidation-reduction reactions. Biochem J 84:368-382.
18. Ou X, et al. (2006) Crystal structures of human glycerol 3-phosphate dehydrogenase 1 (GPD1). J Mol Biol 357:858-869.
19. Zhang J, Frerman FE, Kim JJ (2006) Structure of electron transfer flavoproteinubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool. Proc Natl Acad Sci USA 103:16212-16217.
20. Ye S, et al. (2001) The structure of a Michaelis serpin-protease complex. Nat Struct Biol 8:979-983.
21. Ponstingl H, Henrick K, Thorton JM (2000) Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins Struct Funct Genet 41:47-57.
22. Elcock AH, McCammon JA (2001) Identification of protein oligomerization states by analysis of interface conservation. Proc Natl Acad Sci USA 98:2990-2994.
23. Fraaije MW, Mattevi A (2000) Flavoenzymes: diverse catalysts with recurrent features. Trends Biochem Sci 25:126-132.
24. Ghanem M, Gadda G (2006) Effects of reversing the protein positive charge in the proximity of the flavin N (1) locus of choline oxidase. Biochemistry 45:3437-3447.
25. Pollegioni L, Blodig W, Ghisla S (1997) On the mechanism of D-amino acid oxidase. Structure/linear free energy correlations and deuterium kinetic isotope effects using substituted phenylglycines. J Biol Chem 272:4924-4934.
26. Lee L-H, Nadaraia S, Gu D, Becker DF, Tanner JJ (2003) Structure of the proline dehydrogenase domain of the multifunctional PutA flavoprotein. Nat Struct Biol 10:109-114.
27. Huang L-S, et al. (2006) 3-Nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme. J Biol Chem 281:5965-5972.
28. Taylor P, Pealing SL, Reid GA, Chapman SK, Walkinshaw MD (1999) Structural and mechanistic mapping of a unique fumarate reductase. Nat Struct Biol 6:1108-1112.
29. Hedstrom L, Gan, L. (2006) IMP dehydrogenase: Structural schizophrenia and an unusual base. Curr Opin Chem Biol 10:520-525.
30. Yue QK, Kass IJ, Sampson NS, Vrielink A (1999) Crystal structure determination of cholesterol oxidase from Streptomyces and structural characterization of key active site mutants. Biochemistry 38:4277-4286.
31. Lenaz G (2001) A critical appraisal of the mitochondrial coenzyme Q pool. FEBS Lett 509:151-155.
32. Iwata S, et al. (1998) Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex. Science 281:64-71.
33. Rowland P, Nielsen FS, Jensen KF, Larsen S (1997) The crystal structure of the flavin containing enzyme dihydroorotate dehydrogenase A from Lactococcus lactis. Structure (London) 5:239-252.
34. Grigorieff N, Ceska TA, Downing KH, Baldwin JM, Henderson R (1996) Electroncrystallographic refinement of the structure of bacteriorhodopsin. J Mol Biol 259:393-421.
35. Leite JF, Amoscato AA, Cascio M (2000) Coupled proteolytic and mass spectrometry studies indicate a novel topology for the glycine receptor. J Biol Chem 275:13683-13689.
36. Leucke H, Schobert B, Richter HT, Cartailler JP, Lanyi JK (1999) Structure of bacteriorhodopsin at 1.55 A resolution. J Mol Biol 291:899-911.
37. Hara-Chikuma M, et al. (2005) Progressive adipocyte hypertrophy in aquaporin-7-deficient mice: Adipocyte glycerol permeability as a novel regulator of fat accumulation. J Biol Chem 280:15493-15496.
38. Maeda N, et al. (2004) Adaptation to fasting by glycerol transport through aquaporin 7 in adipose tissue. Proc Natl Acad Sci USA 101:17801-17806.
39. Hakimi P, et al. (2007) Overexpression of the cytosolic form of phosphoenolpyruvate carboxykinase (GTP) in skeletal muscle repatterns energy metabolism in the mouse. J Biol Chem 282:32844-32855.
40. Yeh JI, Du S, Tortajada A, Paulo J, Zhang S (2005) Peptergents: Peptide detergents that improve stability and functionality of an integral membrane protein, glycerol-3-phosphate dehydrogenase. Biochemistry 44:16912-16919.
41. Otwinowski Z, Minor W (1997) Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307-327.
42. Pflugrath JW (1999) The finer things in x-ray diffraction data collection. Acta Crystallogr D 55:1718-1725
43. Terwilliger TC, Berendzen J (1999) Automated MAD, MIR structure solution. Acta Crystallogr D 55:849-861
44. Murshudov, GN, Vagin AA, Dodson EG (1997) Refinement of macromolecular structures by maximum likelihood method. Acta Crystallogr D 53:240-255.
45. Brunger AT, et al. (1998) Crystallography and NMR system: A new software system for macromolecular structure determination. Acta Crystallogr D 54:905-921.
46. Perrakis A, Sixma TK, Wilson KS, Lamzin VS (1997) wARP: Improvement and extension of crystallographic phases by weighted averaging of multiple refined dummy atomic models. Acta Crystallogr D 53:448-455.