Sandbox 160

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Glyceraldehyde 3-Phosphate Dehydrogenase

Introduction

PDB ID 1vc2

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1vc2, resolution 2.60Å ()
Ligands:
Activity: Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), with EC number 1.2.1.12
Resources: FirstGlance, OCA, RCSB, PDBsum, TOPSAN
Coordinates: save as pdb, mmCIF, xml


Glyceraldehyde 3-Phosphate dehydrogenase (GAPDH) is an Oxidoreductase enzyme involved in many important biochemical reactions and belongs to the Aldehyde Dehydrogenase superfamily[1]. GAPDH has been divided into two large classes and subsequent subclasses. Class 1 consists of eukaryotes and eubacteria whereas class 2 contains archael GAPDHs [2]. It is involved in glycolysis, gluconeogenesis and in the case of photosynthetic organisms, the carbon reduction cycle [2]. This protein is responsible for catalyzing the conversion of glyceraldeyde 3-Phosphate into 1,3-Biphosphoglycerate in a two step coupled mechanism. This conversion occurs during step 6 or the beginning of the "payoff phase" of glycolysis (the second half of the entire process) in which ATP and NADH is produced. A total of 2 NADH and 4 ATP are produced during this phase for a net gain of 2 NADH and 2 ATP for the entire glycolysis pathway per glucose.A number of disease causing parasites particularly protists such as Trypanosoma brucei rely on glycolysis to provide the energy for their biochemical functions. Due to this, such parasites will heavily rely on GAPDH due to its intrinsic role in the glycolytic pathway and therefore targeting this enzyme complex can be a promising field of research. Subsequent pharmaceutical drug development and testing can then be conducted to provide protection against deadly viruses and disease. This protein has also been linked as acting as a nitric oxide sensor and plays roles in transcriptional regulation of genes along with translational silencing [3]. Although the exact mechanism of these roles are unknown at the moment it is believed that posttranslational modifications play a part in determining these alternative functions[3].

Structure & Function

Glyceraldehyde 3-Phosphate Dehydrogenase (GAPDH)has carefully been studied in a number of bacterial, parasitic and mammalian species and it has been found that it exists as homotetrameric protein [4]. Each subunit within the protein is 38,151Da (tetramer is 152.4 kDa)and contains seven alpha helices and two beta sheets, one of which has seven strands and the other with eight[4] [5]. Two anion binding sites have been found where the two phosphates involved in the reaction will be bound during catalysis. One site is labeled "Pi" and is the location where the inorganic phosphate involved will bind and the other has been labeled "Ps" which is where the C-3 phosphate of Gylceraldeyhde 3-Phosphate will bind [4]. Further experimentation has shown that the "Ps" site has been conserved in numerous GAPDH complexes and that the former may involve two possible sites in which the second or new "Pi" site is located 2.9 Angstroms from the primary "Pi" site[4].

The enzyme contains a functional NAD+ group which functions as a hydrogen acceptor during the course of the reaction which is bound to a Rossman fold. During the catalysis of glyceraldehyde 3-phosphate to 1,3-biphosphoglycerate a hydride ion is enzymatically transferred from the aldehyde group of glyceraldehyde 3-phosphate to the nicotinamide ring of NAD+ reducing it to NADH[4]. The active site of GAPDH contains a cysteine (Cys149) residue which reacts with the Glyceraldehyde 3-Phosphate molecule through its -SH group. The substrate is covalently bound during the reaction through its aldehyde group to the -SH group of the cysteine residue and the resulting reaction produces a thiohemiacetal intermediate [4]. Note that this reaction occurs through acid base catalysis with aid of a histidine residue (His176).The of the molecule is illustrated to the right.

A simplified illustration of the net reaction is as follows: 

    D-glyceraldehyde 3-phosphate + phosphate + NAD+ ---------> 1,3 biphospho-D-glycerate + NADH + H+

The inorganic phosphate (Pi) that is involved in the reaction functions to attack by phosphorolysis, the thioester intermediate that is formed by the substrate on the cysteine reside after NAD+ has been reduced [4]. The attack by Pi on the carbonyl carbon of C1 is simultaneously followed by the replacement of bound NADH for NAD+ so another turn of the cycle can now commence. The final product is released as 1,3 bisphosphoglycerate in which the second Pi molecule has been incorporated[4].


Active Site in Detail

Figure 1. Illustration created using PDB software highlighting the NAD+ ligand and Cysteine and Histidine residues within the active site of 1vc2.
Figure 1. Illustration created using PDB software highlighting the NAD+ ligand and Cysteine and Histidine residues within the active site of 1vc2.
Once Glyceraldehyde 3-phophate comes into contact with the active site it forms a hydrogen bond through its C2 hydroxyl group to Cys149N (Cys149=green). The C1 hydroxyl group of the substrate binds to His176NE2 (His176=teal)[6]. Additional hydrogen bonds to the phosphate group of the substrate from additional residues such as Thr1790G1, Arg231NH1(these two residues are not highlighted in figure 1) along with N7N and 02'N of the NAD+ moeity (NAD+=pink) help stabilize the molecule during the course of the reaction in the active site [6]. The nicotinamide ring of the NAD+ ligand is responsible for orienting the hydrogen atom at C1 towards itself which allows for easier transfer in producing in reducing NAD+ to NADH. The positive charge that arises when NADH is formed helps to stabilize the negatively charged oxygen on the carbonyl group that is present in the active site. Usually the holoenzyme form of GAPDH is found to contain NAD+ in two or three of its active sites, however in the protozoan parasite Cryptosporidium parvum NAD+ is found to be bound in each subunit (all 4) [4]. Binding of NAD+ to its designated subunit is known to cause a conformational change in that individual subunit and cause distances between residues to change. This is seen in E. coli in which it is known that upon the binding of the ligand (NAD+), the distance between the thiol group of the cysteine residue and the NE2 of the histidine increases within the active site[4]. This movement and subsequent differences between residues in the active site or at other locations is thought to occur to support the NAD+ molecule and allow for hydrophobic interactions with the its ring[4]. The movement of residues 77-83 in C. parvum maneuvers an important oxygen of residue K79 so that it is in favorable proximity to hydrogen bond with AN6 located on the ligand molecule[4]. Class II (Archael) GAPDHs have also been studied in detail and show interesting and definite properties. High concentrations of NADP(H) along with ATP and NADH have been found to reduce the enzymes affinity for NAD+, whereas glucose 1-phosphate, fructose 6-phosphate, AMP and ADP show to increase the affinity between the two as evidenced by the studies performed on Thermoproteus tenax[1].

Relations to Medicine

Strong structural analysis and in depth studies of parasitic protozoans has allowed the determination of conservation and differences between the parasite and human forms of GAPDH. Trypanosoma cruzi, a protozoan parasite is responsible for causing Chagas' disease in approximately 16-18 million people from southern and central America[7]. This parasite is responsible for causing up to 45,000 deaths per year and can cause severe complications such as neurological disorders and chronic cardiopathy[7]. Although there are preexisting drugs on the market that do show some effectiveness, they are all known to cause severe side effects which defeats the purpose of their production. The role of Glyceraldehyde 3-Phosphate Dehydrogenase in this case is that it has been found that the bloodstream forms of the related protozoan T. bruceiare shown to lack a functional tricarboxylic acid cycle and thus its ultimate ATP source must come from glycolysis[7]. It is this finding that has intrigued scientists to find solutions to the diseases caused by these protozoans. At the moment the most relevant target is the binding site of the adenosine ring of the NAD+ cofactor. It has been studied in great detail and its differences from the human form have been well recorded to allow the outcome of a possible solution[7]. The NAD+ binding region is homologous in both T. brucei and T. cruzi and this site is therefore a suitable target for inhibitors that will provide a solution to Chagas' disease[7]. This step will be advantageous because several adenosine analogues have already been designed and applied as selective and competitive inhibitors to trypanosomatid GAPDHs and have shown to stop the growth of T. brucei within the bloodstream[8].

Research relating oxidative stress to GAPDH has also been conducted and shows very promising results. Nitration of tyrosine residues is a sign that oxidative stress is occuring, and nitration of tyrosine has been known to be linked to neurodegenerative disorders and cancer[3]. It has been documented that nitration of the cysteine (Cys149) residue within the active site of the GAPDH enzyme is responsible for causing loss of enzymatic activity[3]. This loss of enzymatic activity is due to the nitration of two tyrosine residues (Tyr311 and Tyr317) which are in close proximity to the active site cysteine. The ultimate result of this nitration is that it causes the loss of affinity for NAD+ and therefore a loss of NAD+ binding[3]. The insoluble aggregates that are found in Alzheimer's and Parkinson's disease are due to intramolecular disulfide bond formation within the GAPDH, as a consequence of oxidative stress which causes the aggregation and accumulation of the protein within the cell, thus contributing to the diseases[9].

References

  1. ↑ 1.0 1.1 Brunner NA, Brinkmann H, Siebers B, Hensel R. NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase from Thermoproteus tenax. The first identified archaeal member of the aldehyde dehydrogenase superfamily is a glycolytic enzyme with unusual regulatory properties. J Biol Chem. 1998 Mar 13;273(11):6149-56. PMID:9497334
  2. ↑ 2.0 2.1 Fermani S, Ripamonti A, Sabatino P, Zanotti G, Scagliarini S, Sparla F, Trost P, Pupillo P. Crystal structure of the non-regulatory A(4 )isoform of spinach chloroplast glyceraldehyde-3-phosphate dehydrogenase complexed with NADP. J Mol Biol. 2001 Nov 30;314(3):527-42. PMID:11846565 doi:10.1006/jmbi.2001.5172
  3. ↑ 3.0 3.1 3.2 3.3 3.4 Palamalai V, Miyagi M. Mechanism of glyceraldehyde-3-phosphate dehydrogenase inactivation by tyrosine nitration. Protein Sci. 2010 Feb;19(2):255-62. PMID:20014444 doi:10.1002/pro.311
  4. ↑ 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 4.11 Cook WJ, Senkovich O, Chattopadhyay D. An unexpected phosphate binding site in glyceraldehyde 3-phosphate dehydrogenase: crystal structures of apo, holo and ternary complex of Cryptosporidium parvum enzyme. BMC Struct Biol. 2009 Feb 25;9:9. PMID:19243605 doi:10.1186/1472-6807-9-9
  5. ↑ Senkovich O, Speed H, Grigorian A, Bradley K, Ramarao CS, Lane B, Zhu G, Chattopadhyay D. Crystallization of three key glycolytic enzymes of the opportunistic pathogen Cryptosporidium parvum. Biochim Biophys Acta. 2005 Jun 30;1750(2):166-72. PMID:15953771 doi:10.1016/j.bbapap.2005.04.009
  6. ↑ 6.0 6.1 Song SY, Xu YB, Lin ZJ, Tsou CL. Structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor. J Mol Biol. 1999 Apr 9;287(4):719-25. PMID:10191140 doi:http://dx.doi.org/10.1006/jmbi.1999.2628
  7. ↑ 7.0 7.1 7.2 7.3 7.4 Souza DH, Garratt RC, Araujo AP, Guimaraes BG, Jesus WD, Michels PA, Hannaert V, Oliva G. Trypanosoma cruzi glycosomal glyceraldehyde-3-phosphate dehydrogenase: structure, catalytic mechanism and targeted inhibitor design. FEBS Lett. 1998 Mar 13;424(3):131-5. PMID:9580189
  8. ↑ Bressi JC, Verlinde CL, Aronov AM, Shaw ML, Shin SS, Nguyen LN, Suresh S, Buckner FS, Van Voorhis WC, Kuntz ID, Hol WG, Gelb MH. Adenosine analogues as selective inhibitors of glyceraldehyde-3-phosphate dehydrogenase of Trypanosomatidae via structure-based drug design. J Med Chem. 2001 Jun 21;44(13):2080-93. PMID:11405646
  9. ↑ Nakajima H, Amano W, Fujita A, Fukuhara A, Azuma YT, Hata F, Inui T, Takeuchi T. The active site cysteine of the proapoptotic protein glyceraldehyde-3-phosphate dehydrogenase is essential in oxidative stress-induced aggregation and cell death. J Biol Chem. 2007 Sep 7;282(36):26562-74. Epub 2007 Jul 5. PMID:17613523 doi:10.1074/jbc.M704199200
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