2-Dehydro-3-deoxy-phosphogluconate aldolase

Class of enzymes 2-dehydro-3-deoxy-phosphogluconate aldolase 4.1.2.14 9024-53-7 0008675 KDPG Aldolase Structure.png The enzyme 2-dehydro-3-deoxy-phosphogluconate aldolase (4.1.2.14), commonly known as KDPG aldolase, catalyzes the chemical reaction 2-dehydro-3-deoxy-D-gluconate 6-phosphate pyruvate + D-glyceraldehyde 3-phosphate This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. It is used in the Entner–Doudoroff pathway in prokaryotes, feeding into glycolysis. 2-dehydro-3-deoxy-phosphogluconate aldolase is one of the two enzymes distinguishing this pathway from the more commonly known Embden–Meyerhof–Parnas pathway.Peekhaus N, Conway T What's for dinner?: Entner–Doudoroff metabolism in Escherichia coli J. Bacteriol. 180 14 3495–502 July 1998 9657988 107313 10.1128/JB.180.14.3495-3502.1998 This enzyme also participates in following 3 metabolic pathways: pentose phosphate pathway, pentose and glucuronate interconversions, and arginine and proline metabolism. In addition to the cleavage of 2-dehydro-3-deoxy-D-gluconate 6-phosphate, it is also found to naturally catalyze Schiff base formation between a lysine ε-amino acid group and carbonyl compounds, decarboxylation of oxaloacetate, and exchange of solvent protons with the methyl hydrogen atoms of pyruvate. Nomenclature The systematic name of this enzyme class is 2-dehydro-3-deoxy-D-gluconate-6-phosphate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming). Other names in common use include: KDPG aldolase phospho-2-keto-3-deoxygluconate aldolase phospho-2-keto-3-deoxygluconic aldolase 2-keto-3-deoxy-6-phosphogluconic aldolase 2-keto-3-deoxy-6-phosphogluconate aldolase 6-phospho-2-keto-3-deoxygluconate aldolase ODPG aldolase, 2-oxo-3-deoxy-6-phosphogluconate aldolase 2-keto-3-deoxygluconate-6-P-aldolase 2-keto-3-deoxygluconate-6-phosphate aldolase 2-dehydro-3-deoxy-D-gluconate-6-phosphate D-glyceraldehyde-3-phosphate-lyase Enzyme structure thumb|upright=2.0|right| Active site structure with bound pyruvate (colors correspond to secondary structure, with cyan, magenta, and light pink referring to helices, sheets, and loops respectively) KDPG Aldolase was recently determined to be a trimer through crystallographic three-fold symmetry, with 225 residues.Mavridis IM, Tulinsky A The folding and quaternary structure of trimeric 2-keto-3-deoxy-6-phosphogluconic aldolase at 3.5-A resolution Biochemistry 15 20 4410–7 October 1976 974067 10.1021/bi00665a010 Mavridis IM, Hatada MH, Tulinsky A, Lebioda L Structure of 2-keto-3-deoxy-6-phosphogluconate aldolase at 2 . 8 A resolution J. Mol. Biol. 162 2 419–44 December 1982 7161801 10.1016/0022-2836(82)90536-8 The enzyme was determined to have a molecular weight of 23,942.Suzuki N, Wood WA Complete primary structure of 2-keto-3-deoxy-6-phosphogluconate aldolase J. Biol. Chem. 255 8 3427–35 April 1980 10.1016/S0021-9258(19)85716-2 6988426 free The trimer is stabilized primarily through hydrophobic interactions. The molecule has tertiary folding similar to triosephosphate isomerase and the A-domain of pyruvate kinase, forming an eight strand α/β-barrel structure.Richardson JS The singly-wound parallel beta barrel: a proposed structure for 2-keto-3-deoxy-6-phosphogluconate aldolase Biochem. Biophys. Res. Commun. 90 1 285–90 September 1979 496979 10.1016/0006-291X(79)91622-X 1979BBRC...90..285R The α/β-barrel structure is capped on one side by the N-terminal helix. The other side, the carboxylic side, contains the active site.Bell BJ, Watanabe L, Rios-Steiner JL, Tulinsky A, Lebioda L, Arni RK Structure of 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida Acta Crystallogr. D 59 Pt 8 1454–8 August 2003 12876349 10.1107/S0907444903013192 Each subunit contains a phosphate-ion bound in position of the aldolase binding site. It has been found that there are four cysteinyl groups present in each subunit, with two readily accessible and two buried in the subunit.Möhler H, Decker K, Wood WA Structure of 2-keto-3-deoxy-6-phosphogluconate aldolase. IV. Structural features revealed by treatment with urea and Ellman's reagent Arch. Biochem. Biophys. 151 1 251–60 July 1972 5044518 10.1016/0003-9861(72)90495-x The active site contains the zwitterionic pair Glu-45/Lys-133. The Lysine, which is involved in the formation of the Schiff base is coordinated by a phosphate ion and two solvent water molecules. The first water molecule serves as a shuttle between the Glutamate and the substrate, staying bound to the enzyme throughout the catalytic cycle. The second water molecule is a product of the dehydration of the carbinolamine that leads to the formation of the Schiff base. It also functions as the nucleophile during hydrolysis of the enzyme-product Schiff base, leading to the release of pyruvate. As of late 2007, 13 structures have been solved for this class of enzymes, with PDB accession codes 1EUA, 1EUN, 1FQ0, 1FWR, 1KGA, 1MXS, 1WA3, 1WAU, 1WBH, 2C0A, 2NUW, 2NUX, and 2NUY. Enzyme mechanism thumb|upright=1.8|left| Active site showing interaction of pyruvate with zwitterionic pair Glu-45/Lys-133 One of the reactions KDPG Aldolase catalyzes, as in the Entner–Doudoroff pathway, is the reversible cleavage of 2-keto-3-deoxy-6-phosphogluconate (KDPG) into pyruvate and D-glyceraldehyde-3-phosphate.Allard J, Grochulski P, Sygusch J Covalent intermediate trapped in 2-keto-3-deoxy-6- phosphogluconate (KDPG) aldolase structure at 1.95-A resolution Proc. Natl. Acad. Sci. U.S.A. 98 7 3679–84 March 2001 11274385 31111 10.1073/pnas.071380898 free 2001PNAS...98.3679A Meloche HP, Glusker JP Aldolase catalysis: single base-mediated proton activation Science 181 4097 350–2 July 1973 4719907 10.1126/science.181.4097.350 1973Sci...181..350M 37940739 This occurs through a stereospecific retro-aldol cleavage.Fullerton SW, Griffiths JS, Merkel AB Mechanism of the Class I KDPG aldolase Bioorg. Med. Chem. 14 9 3002–10 May 2006 16403639 10.1016/j.bmc.2005.12.022 3315828 etal A proton transfer between the zwitterionic pair Glu-45/Lys-133 in the active site activates Lysine to serve as the nucleophile in the first step and Glutamate to aid in the base catalysis involved in the carbon-carbon cleavage. Lysine Residue 133 serves as the nucleophile and attacks the carbonyl group of 2-Keto-3-deoxy-6-phosphogluconate to form a protonated carbinolamine intermediate, also known as a Schiff base intermediate. The intermediate is stabilized by hydrogen bonding with residues in the active site. A three carbon residue, glyceraldehyde 3-phosphate, is cleaved off through base catalysis with a water molecule and residue Glu-45. The pyruvate is generated through the nucleophilic attack of water on the Schiff-base to reform a ketone. Aromatic interaction with Phe-135 ensures the stereospecific addition involved in the reverse process. KDPG aldolase has also been shown to catalyze the exchange of hydrogen atoms of the methyl groups of pyruvate with protons of the solvent. thumb|upright=3|center| KDPG aldolase mechanism in the Entner–Doudoroff pathway Evolutionary significance History Arguments have been made for both the convergent and divergent evolution of α/β-barrel structured enzymes such as KDPG Aldolase, triosephosphate isomerase, and the A-domain of pyruvate kinase. Convergent evolution can lead to geometrically similar active sites while each enzyme has a distinct backbone conformation. Convergence to a common backbone structure, as is the case here however, has not been observed, although it is argues that it might be possible for a symmetrically repetitive structure as the one observed here.Lebioda L, Hatada MH, Tulinsky A, Mavridis IM Comparison of the folding of 2-keto-3-deoxy-6-phosphogluconate aldolase, triosephosphate isomerase and pyruvate kinase. Implications in molecular evolution J. Mol. Biol. 162 2 445–58 December 1982 7161802 10.1016/0022-2836(82)90537-X The similarity in the folding of the three enzymes and the exceptional symmetry commonly suggests divergent evolution from a common ancestor. The functional similarity of the enzymes remains the strongest argument for divergent evolution. All three enzymes activate a C–H bond adjacent to a carbonyl group. The active sites are located at the carboxylic ends of the β strands. Such congruence is in favor of divergent evolution. Should the divergent evolution hypothesis prevail, this would suggest the existence of a class of enzymes with unrelated amino acid sequences yet analogous symmetrical structure and folding. Directed Evolution KDPG aldolase has limited utility due to its high specificity for its natural substrates in the cleavage of KDPG and the reverse addition of D-glyceraldehyde-3-phosphate and pyruvate.Farinas ET, Bulter T, Arnold FH Directed enzyme evolution Curr. Opin. Biotechnol. 12 6 545–51 December 2001 11849936 10.1016/S0958-1669(01)00261-0 In vitro evolution has allowed KDPG aldolase to be converted into a more efficient aldolase with altered substrate specificity and stereoselectivity thereby improving its utility in asymmetric synthesis.Fong S, Machajewski TD, Mak CC, Wong C Directed evolution of D-2-keto-3-deoxy-6-phosphogluconate aldolase to new variants for the efficient synthesis of D- and L-sugars Chem. Biol. 7 11 873–83 November 2000 11094340 10.1016/S1074-5521(00)00035-1 free Rather than modifying the recognition site, the substrate is modified by moving the active site lysine from one β strand to a neighboring one.Wymer N, Buchanan LV, Henderson D Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli Structure 9 1 1–9 January 2001 11342129 10.1016/S0969-2126(00)00555-4 etal free The evolved aldolase is capable of accepting both D- and L-glyceraldehyde in their non-phosphorylated form.Huisman GW, Gray D Towards novel processes for the fine-chemical and pharmaceutical industries Curr. Opin. Biotechnol. 13 4 352–8 August 2002 12323358 10.1016/S0958-1669(02)00335-X References 1 Further reading Meloche HP, Wood WA 1964 Crystallization and characteristics of 2-keto-3-deoxy-6-phosphogluconic aldolase J. Biol. Chem. 239 10 3515–3518 10.1016/S0021-9258(18)97753-7 14245411 free External links Biology no Category:EC 4.1.2 Category:Enzymes of known structure